Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 140 of 170
Found at i:42407490 original size:16 final size:17
Alignment explanation
Indices: 42407416--42407492 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 17
42407406 TAAGATAACA
42407416 TTTAAATAAATATAT-GT
1 TTTAAA-AAATATATAGT
* *
42407433 TTTAAAAATTATTTAGT
1 TTTAAAAAATATATAGT
*
42407450 TTTAAAACAAAGAAATATCAGT
1 TTT--AA-AAA-ATATAT-AGT
42407472 TTTAAAAAATATATA-T
1 TTTAAAAAATATATAGT
42407488 TTTAA
1 TTTAA
42407493 GAATATTAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
16 12 0.25
17 12 0.25
18 5 0.10
19 5 0.10
20 5 0.10
21 3 0.06
22 6 0.12
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (17 bp):
TTTAAAAAATATATAGT
Found at i:42408210 original size:15 final size:14
Alignment explanation
Indices: 42408190--42408230 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 14
42408180 AAGGTTGGGT
42408190 TTTAGGGTTTATATA
1 TTTAGGGTTTAT-TA
42408205 TTTAGGGGTCTTATTA
1 TTTA-GGGT-TTATTA
42408221 TTTAGGGTTT
1 TTTAGGGTTT
42408231 GAGGGTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
16 10 0.42
17 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTATTA
Found at i:42408802 original size:22 final size:21
Alignment explanation
Indices: 42408776--42408875 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 21
42408766 TCAAGATAAA
42408776 TATTAAATTAAATATTAAATCT
1 TATTAAATTAAATATTAAAT-T
*
42408798 TATTAAATT-AATA-GAATATT
1 TATTAAATTAAATATTAA-ATT
* * *
42408818 TATTTACAAGATAAACAATAAATT
1 TA-TTA-AA-TTAAATATTAAATT
*
42408842 AAATTAAATTAAATATTAAATCT
1 -TATTAAATTAAATATTAAAT-T
42408865 TATTAAATTAA
1 TATTAAATTAA
42408876 TAAAATATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.08
21 9 0.15
22 31 0.51
23 4 0.07
24 9 0.15
25 3 0.05
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (21 bp):
TATTAAATTAAATATTAAATT
Found at i:42408856 original size:67 final size:67
Alignment explanation
Indices: 42408777--42408922 Score: 256
Period size: 67 Copynumber: 2.1 Consensus size: 67
42408767 CAAGATAAAT
*
42408777 ATTAAATTAAATATTAAATCTTATTAAATTAATAGAATATTTATTTACAAGATAAACAATAAATT
1 ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACAATAAATT
42408842 AA
66 AA
*
42408844 ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACATTAAATT
1 ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACAATAAATT
42408909 AA
66 AA
42408911 ATTTAATATTAA
1 A-TTAA-ATTAA
42408923 GATAATTACT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
67 66 0.88
68 4 0.05
69 5 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (67 bp):
ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACAATAAATT
AA
Found at i:42408859 original size:57 final size:51
Alignment explanation
Indices: 42408742--42408862 Score: 134
Period size: 57 Copynumber: 2.2 Consensus size: 51
42408732 TAATCATTTT
* * *
42408742 AATATTAAATTAATATAATATTTATCAAGATAAATATTAAATTAAATATTA
1 AATATTAAATTAATAGAATATTTATCAAGATAAACAATAAATTAAATATTA
42408793 AATCTTATTAAATTAATAGAATATTTATTTACAAGATAAACAATAAATTAAATTAAATTA
1 AA---TATTAAATTAATAGAATATTTA--T-CAAGATAAACAATAAATTAAA-T--ATTA
42408853 AATATTAAAT
1 AATATTAAAT
42408863 CTTATTAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
51 2 0.03
54 21 0.36
56 1 0.02
57 27 0.47
58 1 0.02
60 6 0.10
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (51 bp):
AATATTAAATTAATAGAATATTTATCAAGATAAACAATAAATTAAATATTA
Found at i:42409388 original size:19 final size:19
Alignment explanation
Indices: 42409364--42409400 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
42409354 AAAATATCAT
42409364 ATTAATTTTAA-TTAATTTG
1 ATTAA-TTTAATTTAATTTG
42409383 ATTAATTTAATTTAATTT
1 ATTAATTTAATTTAATTT
42409401 AATTTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTAATTTAATTTAATTTG
Found at i:42409394 original size:5 final size:5
Alignment explanation
Indices: 42409365--42409405 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
42409355 AAATATCATA
*
42409365 TTAATT TTAA- TTAAT TTGA- TTAAT TTAAT TTAAT TTAAT TT
1 TTAA-T TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
42409406 TATCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
4 7 0.23
5 20 0.65
6 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:42409405 original size:10 final size:9
Alignment explanation
Indices: 42409364--42409404 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
42409354 AAAATATCAT
42409364 ATTAATTTTA
1 ATTAA-TTTA
*
42409374 ATTAATTTG
1 ATTAATTTA
42409383 ATTAATTTA
1 ATTAATTTA
42409392 ATTTAATTTA
1 A-TTAATTTA
42409402 ATT
1 ATT
42409405 TTATCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (9 bp):
ATTAATTTA
Found at i:42416960 original size:14 final size:14
Alignment explanation
Indices: 42416941--42416967 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42416931 ATATTTTTTT
42416941 TCCATAAATTGAAA
1 TCCATAAATTGAAA
42416955 TCCATAAATTGAA
1 TCCATAAATTGAA
42416968 CCATCCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (14 bp):
TCCATAAATTGAAA
Found at i:42417602 original size:24 final size:24
Alignment explanation
Indices: 42417557--42417602 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
42417547 TAACAGTTTT
* *
42417557 AGAAGGAGCTGGTGAAGTAGGATC
1 AGAAGGAGCTAGTGAAGCAGGATC
*
42417581 AGAAGGAGCTAGTGGAGCAGGA
1 AGAAGGAGCTAGTGAAGCAGGA
42417603 GTTGCTGCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.43, T:0.13
Consensus pattern (24 bp):
AGAAGGAGCTAGTGAAGCAGGATC
Found at i:42421504 original size:56 final size:50
Alignment explanation
Indices: 42421418--42421658 Score: 187
Period size: 50 Copynumber: 4.7 Consensus size: 50
42421408 ATTTGGGTAA
* ** * *
42421418 AGAGATCCCATGTAAGACCATAACTAGGACATGGAATTGACATCATTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGAATTGACA-C--CGAGA-C--G
** *
42421474 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGAATTGACACCGAGACG
* * ** *
42421524 AAAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTCG-CACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGAATT-GACACCGAGACG
* * * * * * * *
42421574 AGAGGTCCCCTGTAAGATCATGTATGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGAATTGACACCGAGACG
** *
42421624 AGAACATCCCATGTAAGACCATGTCTAGGACATGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGG
42421659 CTTTGGCATG
Statistics
Matches: 157, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 88 0.56
51 27 0.17
52 1 0.01
53 4 0.03
55 1 0.01
56 35 0.22
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGAATTGACACCGAGACG
Found at i:42421535 original size:50 final size:50
Alignment explanation
Indices: 42421471--42421666 Score: 248
Period size: 50 Copynumber: 3.9 Consensus size: 50
42421461 CATTGAGATC
*
42421471 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * *
42421521 ACGAAAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTCGCACCGAG
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * * * * * *
42421571 ATGAGAGGTCCCCTGTAAGATCATGTATGGGACATGGCATGGGCACCGAT
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * *
42421621 ATGAGAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 ATGA-AAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
42421667 TGTTGTTATC
Statistics
Matches: 122, Mismatches: 23, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
50 90 0.74
51 32 0.26
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:42421602 original size:100 final size:101
Alignment explanation
Indices: 42421471--42421659 Score: 274
Period size: 100 Copynumber: 1.9 Consensus size: 101
42421461 CATTGAGATC
* * * **
42421471 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACGA-AAGGTCCCAT
1 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATGGGCACCGAGACGAGAACATCCCAT
42421535 GTAAGACCATGTCT-GGAACATGGCGTTCGCACCGAG
66 GTAAGACCATGTCTAGG-ACATGGCGTTCGCACCGAG
* * * *
42421571 ATGAGAGGTCCCCTGTAAGATCATGTATGGGACATGGCATGGGCACCGATATGAGAACATCCCAT
1 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATGGGCACCGAGACGAGAACATCCCAT
42421636 GTAAGACCATGTCTAGGACATGGC
66 GTAAGACCATGTCTAGGACATGGC
42421660 TTTGGCATGT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 47 0.60
101 29 0.37
102 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.20
Consensus pattern (101 bp):
ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATGGGCACCGAGACGAGAACATCCCAT
GTAAGACCATGTCTAGGACATGGCGTTCGCACCGAG
Found at i:42424090 original size:21 final size:21
Alignment explanation
Indices: 42424056--42424096 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42424046 GGGGGAAAGT
*
42424056 GGGAAGGAGTAAAAGTTTTGA
1 GGGAAGGAGTAAAAGGTTTGA
42424077 GGGAA-GAGTAAAAAGGTTTG
1 GGGAAGGAGT-AAAAGGTTTG
42424097 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (21 bp):
GGGAAGGAGTAAAAGGTTTGA
Found at i:42424148 original size:9 final size:9
Alignment explanation
Indices: 42424134--42424170 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42424124 TATAGTTTGA
42424134 TATTCGAAT
1 TATTCGAAT
42424143 TATTCGAAT
1 TATTCGAAT
*
42424152 TATTCGAGT
1 TATTCGAAT
42424161 TATTCGAAT
1 TATTCGAAT
42424170 T
1 T
42424171 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42424240 original size:9 final size:9
Alignment explanation
Indices: 42424224--42424254 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42424214 TCGAGTTGAT
42424224 TCGAATAAC
1 TCGAATAAC
*
42424233 TTGAATAAC
1 TCGAATAAC
42424242 TCGAATAAC
1 TCGAATAAC
42424251 TCGA
1 TCGA
42424255 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42424402 original size:13 final size:13
Alignment explanation
Indices: 42424384--42424473 Score: 55
Period size: 13 Copynumber: 7.2 Consensus size: 13
42424374 ATATAAACTG
42424384 TAATATACATACA
1 TAATATACATACA
*
42424397 TAATATATATACA
1 TAATATACATACA
* **
42424410 -AATTTTTA-ACA
1 TAATATACATACA
* *
42424421 GTGATAAACA-ACA
1 -TAATATACATACA
*
42424434 T-ACATACATACA
1 TAATATACATACA
**
42424446 T-GCATACATACA
1 TAATATACATACA
42424458 TAATATACATACA
1 TAATATACATACA
42424471 TAA
1 TAA
42424474 ACATTAATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
11 8 0.13
12 22 0.37
13 30 0.50
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (13 bp):
TAATATACATACA
Found at i:42424440 original size:4 final size:4
Alignment explanation
Indices: 42424431--42424472 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
42424421 GTGATAAACA
* *
42424431 ACAT ACAT ACAT ACAT GCAT ACAT ACAT AATAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT ACAT A
42424473 AACATTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:42424568 original size:60 final size:57
Alignment explanation
Indices: 42424457--42424569 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 57
42424447 GCATACATAC
* *
42424457 ATAATATACATACATAAACATTAATAAACAGTCATACACATAATAGTAATATACCAT
1 ATAATATACATACATAAACATGAATAAACAGACATACACATAATAGTAATATACCAT
**
42424514 ATAATATACATACATTAAACATGACATATGCA-ACATACAAACATAATAGTAATATA
1 ATAATATACATACA-TAAACATGA-ATAAACAGACATAC--ACATAATAGTAATATA
42424570 ACACATAACA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 14 0.29
58 13 0.27
59 5 0.10
60 16 0.33
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.27
Consensus pattern (57 bp):
ATAATATACATACATAAACATGAATAAACAGACATACACATAATAGTAATATACCAT
Found at i:42424602 original size:25 final size:24
Alignment explanation
Indices: 42424564--42424649 Score: 88
Period size: 23 Copynumber: 3.6 Consensus size: 24
42424554 ACATAATAGT
*
42424564 AATATA-ACACATAACAAATATACA
1 AATATACATACAT-ACAAATATACA
* *
42424588 AATATACATACATA-ATATATATA
1 AATATACATACATACAAATATACA
*
42424611 TATA-ACATACATACAAATATACA
1 AATATACATACATACAAATATACA
*
42424634 AACATAACATACATAC
1 AATAT-ACATACATAC
42424650 TTAACAGTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
22 9 0.18
23 19 0.38
24 7 0.14
25 15 0.30
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (24 bp):
AATATACATACATACAAATATACA
Found at i:42424647 original size:47 final size:43
Alignment explanation
Indices: 42424545--42424648 Score: 127
Period size: 43 Copynumber: 2.3 Consensus size: 43
42424535 TGACATATGC
* * *
42424545 AACATACAAACATAATAGTAATATAACACATAACAAATATACA
1 AACATACATACATAATAATAATATAACACACAACAAATATACA
* *
42424588 AATATACATACATAATATATATATATAACATACATACAAATATACA
1 AACATACATACATAATA-ATA-ATATAACACACA-ACAAATATACA
42424634 AACATAACATACATA
1 AACAT-ACATACATA
42424649 CTTAACAGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
43 15 0.29
44 2 0.04
45 10 0.20
46 15 0.29
47 9 0.18
ACGTcount: A:0.59, C:0.15, G:0.01, T:0.25
Consensus pattern (43 bp):
AACATACATACATAATAATAATATAACACACAACAAATATACA
Found at i:42424654 original size:13 final size:13
Alignment explanation
Indices: 42424572--42424655 Score: 73
Period size: 13 Copynumber: 6.6 Consensus size: 13
42424562 GTAATATAAC
* *
42424572 ACATAACAAATAT
1 ACATAACATACAT
*
42424585 ACA-AATATACAT
1 ACATAACATACAT
* *
42424597 ACATAATATATAT
1 ACATAACATACAT
*
42424610 ATATAACATACAT
1 ACATAACATACAT
* *
42424623 ACA-AATATACAA
1 ACATAACATACAT
42424635 ACATAACATACAT
1 ACATAACATACAT
*
42424648 ACTTAACA
1 ACATAACA
42424656 GTAAATGTAA
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
12 19 0.34
13 37 0.66
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (13 bp):
ACATAACATACAT
Found at i:42424655 original size:38 final size:38
Alignment explanation
Indices: 42424574--42424648 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
42424564 AATATAACAC
* * * * *
42424574 ATAACAAATATACAAATATACATACATAATATATATAT
1 ATAACATACATACAAATATACAAACATAACATACATAT
42424612 ATAACATACATACAAATATACAAACATAACATACATA
1 ATAACATACATACAAATATACAAACATAACATACATA
42424649 CTTAACAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.27
Consensus pattern (38 bp):
ATAACATACATACAAATATACAAACATAACATACATAT
Found at i:42424747 original size:41 final size:39
Alignment explanation
Indices: 42424702--42424826 Score: 108
Period size: 40 Copynumber: 3.1 Consensus size: 39
42424692 AGCGGCATTT
* * *
42424702 TTAGCGGCGTTTGGACAAAAAACGCCGCTCAAGATCGAGCA
1 TTAGCGGCGTTT--ACAAAAAACGCCGATAAAGATAGAGCA
** *
42424743 TTAGCGGCGCTTTACGTAAAATGCCGATAAAGATAGAGCA
1 TTAGCGGCG-TTTACAAAAAACGCCGATAAAGATAGAGCA
* * * * *
42424783 TTAGCGGCGTTTTCAAGGAAACGCCGCTAAAAAT-GAGAA
1 TTAGCGGCGTTTACAA-AAAACGCCGATAAAGATAGAGCA
42424822 TTAGC
1 TTAGC
42424827 AGTATTTTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
39 13 0.19
40 43 0.63
41 9 0.13
42 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTACAAAAAACGCCGATAAAGATAGAGCA
Found at i:42425400 original size:21 final size:21
Alignment explanation
Indices: 42425348--42425416 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
42425338 AGAGTTTTGA
* * *
42425348 GTTTAGAGTTCATGGTTTACT
1 GTTTAGTGTTTATGGTTTAGT
*
42425369 G-TTCGTGGTTTATGGTTTAGT
1 GTTTAGT-GTTTATGGTTTAGT
42425390 GTTTAGTGTTTA-GTGTTTAGT
1 GTTTAGTGTTTATG-GTTTAGT
*
42425411 GGTTAG
1 GTTTAG
42425417 AAGCATAGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.10
21 31 0.79
22 4 0.10
ACGTcount: A:0.14, C:0.04, G:0.30, T:0.51
Consensus pattern (21 bp):
GTTTAGTGTTTATGGTTTAGT
Found at i:42425436 original size:22 final size:22
Alignment explanation
Indices: 42425404--42425456 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
42425394 AGTGTTTAGT
*
42425404 GTTTAGTGGTTAGAAGCATAGG
1 GTTTAGGGGTTAGAAGCATAGG
* * *
42425426 GTTTAGGGGTTATAGGCTTAGG
1 GTTTAGGGGTTAGAAGCATAGG
*
42425448 GTCTAGGGG
1 GTTTAGGGG
42425457 GTCGGGGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.06, G:0.42, T:0.32
Consensus pattern (22 bp):
GTTTAGGGGTTAGAAGCATAGG
Found at i:42425518 original size:23 final size:21
Alignment explanation
Indices: 42425461--42425534 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 21
42425451 TAGGGGGTCG
*
42425461 GGGTTTAG-GGTTTTGGATTTAA
1 GGGTTTAGTGG-TTTGGGTTT-A
42425483 GGGTTTA-TAGGTTATGGGTTTA
1 GGGTTTAGT-GGTT-TGGGTTTA
42425505 GTGGTTTAGTGGTTTAGGGTTTA
1 G-GGTTTAGTGGTTT-GGGTTTA
*
42425528 AGGTTTA
1 GGGTTTA
42425535 AAGTTTAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
22 18 0.41
23 25 0.57
24 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (21 bp):
GGGTTTAGTGGTTTGGGTTTA
Found at i:42425525 original size:15 final size:15
Alignment explanation
Indices: 42425373--42425534 Score: 65
Period size: 15 Copynumber: 11.0 Consensus size: 15
42425363 TTTACTGTTC
*
42425373 GTGGTTTATGGTTTA
1 GTGGTTTAGGGTTTA
*
42425388 GT-GTTTAGTGTTTA
1 GTGGTTTAGGGTTTA
42425402 GT-GTTTAGTGG-TTA
1 GTGGTTTAG-GGTTTA
** **
42425416 GAAGCATAGGGTTTA
1 GTGGTTTAGGGTTTA
* *
42425431 GGGGTTATA-GGCTTA
1 GTGGTT-TAGGGTTTA
* ** *
42425446 G-GGTCTAGGGGGTC
1 GTGGTTTAGGGTTTA
*
42425460 GGGGTTTAGGGTTT-
1 GTGGTTTAGGGTTTA
42425474 -TGGATTTAAGGGTTTA
1 GTGG-TTT-AGGGTTTA
42425490 -TAGG-TTATGGGTTTA
1 GT-GGTTTA-GGGTTTA
42425505 GTGGTTTAGTGGTTTA
1 GTGGTTTAG-GGTTTA
*
42425521 G-GGTTTAAGGTTTA
1 GTGGTTTAGGGTTTA
42425535 AAGTTTAAAG
Statistics
Matches: 113, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
13 4 0.04
14 41 0.36
15 52 0.46
16 14 0.12
17 2 0.02
ACGTcount: A:0.17, C:0.02, G:0.38, T:0.43
Consensus pattern (15 bp):
GTGGTTTAGGGTTTA
Found at i:42425534 original size:14 final size:14
Alignment explanation
Indices: 42425499--42425577 Score: 67
Period size: 14 Copynumber: 5.7 Consensus size: 14
42425489 ATAGGTTATG
*
42425499 GGTTTAGTGGTTTAGT
1 GGTTTAG-GGTTTA-A
42425515 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
**
42425529 GGTTTAAAGTTTAA
1 GGTTTAGGGTTTAA
*
42425543 AGTTTAGGG-TTAA
1 GGTTTAGGGTTTAA
42425556 --TTTAGGGTTTACA
1 GGTTTAGGGTTTA-A
42425569 -GTTTAGGGT
1 GGTTTAGGGT
42425578 ATATGTTTAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
11 7 0.13
12 3 0.06
13 5 0.09
14 26 0.48
15 6 0.11
16 7 0.13
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.44
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:42425565 original size:25 final size:26
Alignment explanation
Indices: 42425537--42425614 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
42425527 AAGGTTTAAA
*
42425537 GTTTAAAGTTTAGGGTTA-ATTTAGG
1 GTTTAAAGTTTAGGGTTATATTTAGC
* *
42425562 GTTTACAGTTTAGGGTATATGTTTAGC
1 GTTTAAAGTTTAGGGT-TATATTTAGC
* *
42425589 GTATAAAGTTTAAGGTTTATGATTTA
1 GTTTAAAGTTT-AGGGTTAT-ATTTA
42425615 ATGTTAAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 15 0.36
26 2 0.05
27 17 0.40
28 8 0.19
ACGTcount: A:0.28, C:0.03, G:0.24, T:0.45
Consensus pattern (26 bp):
GTTTAAAGTTTAGGGTTATATTTAGC
Found at i:42425566 original size:7 final size:7
Alignment explanation
Indices: 42425375--42425553 Score: 67
Period size: 7 Copynumber: 24.6 Consensus size: 7
42425365 TACTGTTCGT
*
42425375 GGTTTAT
1 GGTTTAG
42425382 GGTTTAG
1 GGTTTAG
*
42425389 TGTTTAG
1 GGTTTAG
*
42425396 TGTTTAG
1 GGTTTAG
*
42425403 TGTTTAG
1 GGTTTAG
42425410 TGG-TTAG
1 -GGTTTAG
* **
42425417 AAGCATAG
1 -GGTTTAG
42425425 GGTTTAGG
1 GGTTTA-G
42425433 GGTTATA-
1 GGTT-TAG
*
42425440 GGCTTAG
1 GGTTTAG
*
42425447 GGTCTAGG
1 GGTTTA-G
* **
42425455 GGGTCGG
1 GGTTTAG
42425462 GGTTTAG
1 GGTTTAG
*
42425469 GGTTTTG
1 GGTTTAG
*
42425476 GATTTAAG
1 GGTTT-AG
*
42425484 GGTTTATA
1 GGTTTA-G
42425492 GG-TTATG
1 GGTTTA-G
42425499 GGTTTAG
1 GGTTTAG
42425506 TGGTTTAG
1 -GGTTTAG
42425514 TGGTTTAG
1 -GGTTTAG
*
42425522 GGTTTAA
1 GGTTTAG
*
42425529 GGTTTAA
1 GGTTTAG
* *
42425536 AGTTTAA
1 GGTTTAG
*
42425543 AGTTTAG
1 GGTTTAG
42425550 GGTT
1 GGTT
42425554 AATTTAGGGT
Statistics
Matches: 133, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
6 2 0.02
7 92 0.69
8 37 0.28
9 2 0.02
ACGTcount: A:0.19, C:0.02, G:0.36, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:42426259 original size:115 final size:116
Alignment explanation
Indices: 42425917--42426327 Score: 522
Period size: 115 Copynumber: 3.6 Consensus size: 116
42425907 AGCATAATGG
* * *
42425917 TGTCG-TTTTATCTGCGTTTTTAGTGGCGTTTTTGCTAAAACACCGCAAAAGGATATGTATTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
*
42425981 GGCGTTTTTACAAAAAACGCCGCAATTATGTTTTTAGTCTTTGGTAAACGT
66 GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
* **
42426032 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACCAAAATGCCGCAAAAGGATATGTGTTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
** * * * *
42426097 GGCGTTTTTA-GGAAATCGCCGTAATTGTATTATTAGTCTTTGGTAAACGT
66 GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
* * * * * *
42426147 TGTCGTTTTTATCTACATTATTAGTGGC-TTTTTACTAAAACGCCGCGAAAGGTTATGTGGTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
* * * * * * *
42426211 GGTGTTTTTACAAAAAACGTCGCAATTATGTTATAATTGTTCGCTAAACGT
66 GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
* * ** *
42426262 TGTCGTTTTTATCTACGTTTTTAGTGGTGTTTGTACTAAAACACCGGTAAAGGATATGTTTTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
42426327 G
66 G
42426328 CCGTAATTAC
Statistics
Matches: 250, Mismatches: 43, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
114 40 0.16
115 117 0.47
116 93 0.37
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (116 bp):
TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
Found at i:42427502 original size:30 final size:32
Alignment explanation
Indices: 42427442--42427505 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
42427432 CACTTATTTT
42427442 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
42427475 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
42427506 ACATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:42427766 original size:41 final size:41
Alignment explanation
Indices: 42427721--42427876 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
42427711 ACCGGCTCTT
*
42427721 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
42427762 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
42427803 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
42427844 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
42427877 TAATGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:42435122 original size:32 final size:31
Alignment explanation
Indices: 42435084--42435147 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
42435074 ACACTTATTT
42435084 TCACCTATGCCGAATGCATACACATAAATATA
1 TCACCTATGCCGAATGCA-ACACATAAATATA
* *
42435116 TCACCTATGCCGAATGCAACATATATATATA
1 TCACCTATGCCGAATGCAACACATAAATATA
42435147 T
1 T
42435148 ACATATCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (31 bp):
TCACCTATGCCGAATGCAACACATAAATATA
Found at i:42435407 original size:41 final size:41
Alignment explanation
Indices: 42435362--42435517 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
42435352 ACCGGCTCTT
*
42435362 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
42435403 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
42435444 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
42435485 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
42435518 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:42440184 original size:21 final size:20
Alignment explanation
Indices: 42440160--42440254 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 20
42440150 CTACAACTTA
**
42440160 AAGCAGATGCAGCAGCGAGGG
1 AAGCAGA-GCAGCAGCGAGAC
42440181 AAGCAGAGGCAGCAGCGAGAC
1 AAGCAGA-GCAGCAGCGAGAC
*
42440202 AAGCAGAGGCTA-CAGCAAGAC
1 AAGCAGA-GC-AGCAGCGAGAC
**
42440223 AAGCAGAGACTA-CAGCGAGGG
1 AAGCAGAG-C-AGCAGCGAGAC
42440244 AAGCAGAGCAG
1 AAGCAGAGCAG
42440255 AGCAAAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 60 0.94
22 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.37, T:0.03
Consensus pattern (20 bp):
AAGCAGAGCAGCAGCGAGAC
Found at i:42440698 original size:84 final size:85
Alignment explanation
Indices: 42440588--42440747 Score: 234
Period size: 84 Copynumber: 1.9 Consensus size: 85
42440578 TTTGTGGGAG
* * *
42440588 AAGCGCCGCTAAAAGTCATGATCTATAGCGACGTTTGTGGG-GTAAGCGTCGCTAAAAGTCATGA
1 AAGCGCCGCTAAAAGTCATGACCTATAGCGACGTTTGTGGGAG-AAGCGCCGCTAAAAGTCATAA
*
42440652 TCTATAGCGGCGCTTTTATAC
65 CCTATAGCGGCGCTTTTATAC
** *
42440673 AAGCGCC-CTAAAAGTCATGACCTATAGCGGTGTTTGTGGGAGAAGCGCCGCTAAAGGTCATAAC
1 AAGCGCCGCTAAAAGTCATGACCTATAGCGACGTTTGTGGGAGAAGCGCCGCTAAAAGTCATAAC
42440737 CTATAGCGGCG
66 CTATAGCGGCG
42440748 TTTGTCGGAG
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 59 0.88
85 8 0.12
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (85 bp):
AAGCGCCGCTAAAAGTCATGACCTATAGCGACGTTTGTGGGAGAAGCGCCGCTAAAAGTCATAAC
CTATAGCGGCGCTTTTATAC
Found at i:42440773 original size:43 final size:42
Alignment explanation
Indices: 42440572--42440770 Score: 222
Period size: 43 Copynumber: 4.7 Consensus size: 42
42440562 TTCTTTAGCG
* *
42440572 GCGGTGTTTGTGGGAGAAGCGCCGCTAAAAGTCATGATCTATA
1 GCGGCGTTTGT-GGAGAAGCGCCGCTAAAAGTCATGACCTATA
* * * *
42440615 GCGACGTTTGTGGGGTAAGCGTCGCTAAAAGTCATGATCTATA
1 GCGGCGTTTGTGGAG-AAGCGCCGCTAAAAGTCATGACCTATA
** *
42440658 GCGGCGCTTT-TATACAAGCGCC-CTAAAAGTCATGACCTATA
1 GCGGCG-TTTGTGGAGAAGCGCCGCTAAAAGTCATGACCTATA
* * *
42440699 GCGGTGTTTGTGGGAGAAGCGCCGCTAAAGGTCATAACCTATA
1 GCGGCGTTTGT-GGAGAAGCGCCGCTAAAAGTCATGACCTATA
*
42440742 GCGGCGTTTGTCGGAGAAGCGTCGCTAAA
1 GCGGCGTTTGT-GGAGAAGCGCCGCTAAA
42440771 GGTTATTACT
Statistics
Matches: 131, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
40 3 0.02
41 24 0.18
42 17 0.13
43 84 0.64
44 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (42 bp):
GCGGCGTTTGTGGAGAAGCGCCGCTAAAAGTCATGACCTATA
Found at i:42440787 original size:43 final size:43
Alignment explanation
Indices: 42440572--42440793 Score: 182
Period size: 43 Copynumber: 5.2 Consensus size: 43
42440562 TTCTTTAGCG
* * * *
42440572 GCGGTGTTTGTGGGAGAAGCGCCGCTAAAAGTCATGATCTATA
1 GCGGTGTTTGTCGGAGAAGCGCCGCTAAAGGTCATAACCTATA
** * * * * *
42440615 GCGACGTTTGT-GGGGTAAGCGTCGCTAAAAGTCATGATCTATA
1 GCGGTGTTTGTCGGAG-AAGCGCCGCTAAAGGTCATAACCTATA
* ** * * *
42440658 GCGGCGCTTT-T-ATACAAGCGCC-CTAAAAGTCATGACCTATA
1 GCGGTG-TTTGTCGGAGAAGCGCCGCTAAAGGTCATAACCTATA
*
42440699 GCGGTGTTTGTGGGAGAAGCGCCGCTAAAGGTCATAACCTATA
1 GCGGTGTTTGTCGGAGAAGCGCCGCTAAAGGTCATAACCTATA
* * * * * *
42440742 GCGGCGTTTGTCGGAGAAGCGTCGCTAAAGGTTATTACTTTTA
1 GCGGTGTTTGTCGGAGAAGCGCCGCTAAAGGTCATAACCTATA
42440785 GCGGTGTTT
1 GCGGTGTTT
42440794 ATTTCTAAAA
Statistics
Matches: 149, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
40 3 0.02
41 24 0.16
42 17 0.11
43 102 0.68
44 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (43 bp):
GCGGTGTTTGTCGGAGAAGCGCCGCTAAAGGTCATAACCTATA
Found at i:42440959 original size:5 final size:5
Alignment explanation
Indices: 42440933--42441216 Score: 137
Period size: 5 Copynumber: 58.4 Consensus size: 5
42440923 GTGATACATG
*
42440933 CATAA CAGT-A CATAA CAT-A CATAA CATAA CATAA CAATAAA CGTAA
1 CATAA CA-TAA CATAA CATAA CATAA CATAA CATAA C-AT-AA CATAA
*
42440979 CAT-A CAT-G CATAA CAGT-A CATAA CAT-A CATAA CAT-A CAATAAA
1 CATAA CATAA CATAA CA-TAA CATAA CATAA CATAA CATAA C-AT-AA
* *
42441022 CGTAA CAT-A CA-AA CAAAA CAGT-A CATAA CAT-A CATAA CATAA CAATAAA
1 CATAA CATAA CATAA CATAA CA-TAA CATAA CATAA CATAA CATAA C-AT-AA
* *** *
42441071 CGTAA CAT-A CA-AA CATAA CAGGT CATAA CAT-A CATAA CATAA TAGTAAA
1 CATAA CATAA CATAA CATAA CATAA CATAA CATAA CATAA CATAA CA-T-AA
* *
42441120 CGTAA CAT-A CAT-G CATAA CAGT-A CATAA CAT-A CATAA CATAA CAGTAA
1 CATAA CATAA CATAA CATAA CA-TAA CATAA CATAA CATAA CATAA CA-TAA
* * * *
42441168 AAGTAA CAT-A CGT-A CATAA TAGT-A CATAA CAT-A CATTA CAT-A CATAA
1 CA-TAA CATAA CATAA CATAA CA-TAA CATAA CATAA CATAA CATAA CATAA
42441215 CA
1 CA
42441217 GTTTAAAAAC
Statistics
Matches: 218, Mismatches: 27, Indels: 68
0.70 0.09 0.22
Matches are distributed among these distances:
4 67 0.31
5 119 0.55
6 22 0.10
7 10 0.05
ACGTcount: A:0.54, C:0.20, G:0.06, T:0.20
Consensus pattern (5 bp):
CATAA
Found at i:42441091 original size:49 final size:49
Alignment explanation
Indices: 42440926--42441209 Score: 383
Period size: 49 Copynumber: 5.7 Consensus size: 49
42440916 TGGTGTAGTG
*
42440926 ATACATGCATAACAGTACATAACATACATAACATAACATAACAATAAACGTAAC
1 ATACATACATAACAGTACAT---A-ACAT-ACATAACATAACAATAAACGTAAC
*
42440980 ATACATGCATAACAGTACATAACATACATAACAT-ACAATAAACGTAAC
1 ATACATACATAACAGTACATAACATACATAACATAACAATAAACGTAAC
* *
42441028 ATACAAACAAAACAGTACATAACATACATAACATAACAATAAACGTAAC
1 ATACATACATAACAGTACATAACATACATAACATAACAATAAACGTAAC
* * *
42441077 ATACAAACATAACAGGT-CATAACATACATAACATAATAGTAAACGTAAC
1 ATACATACATAACA-GTACATAACATACATAACATAACAATAAACGTAAC
* * *
42441126 ATACATGCATAACAGTACATAACATACATAACATAACAGTAAAAGTAAC
1 ATACATACATAACAGTACATAACATACATAACATAACAATAAACGTAAC
* * *
42441175 ATACGTACATAATAGTACATAACATACATTACATA
1 ATACATACATAACAGTACATAACATACATAACATA
42441210 CATAACAGTT
Statistics
Matches: 213, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
48 47 0.22
49 139 0.65
50 6 0.03
51 1 0.00
54 20 0.09
ACGTcount: A:0.54, C:0.19, G:0.06, T:0.21
Consensus pattern (49 bp):
ATACATACATAACAGTACATAACATACATAACATAACAATAAACGTAAC
Found at i:42441236 original size:29 final size:32
Alignment explanation
Indices: 42441195--42441273 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 32
42441185 AATAGTACAT
42441195 AACATA-CATTACATACAT-AACAGT-TTAAA-
1 AACATAGCA-TACATACATAAACAGTATTAAAC
42441224 AACATAGCATACATACATAAACAGTAATTAAAC
1 AACATAGCATACATACATAAACAGT-ATTAAAC
*
42441257 ATACATAGCAAACATAC
1 A-ACATAGCATACATAC
42441274 CTTTCACCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 15 0.35
30 8 0.19
32 5 0.12
33 1 0.02
34 14 0.33
ACGTcount: A:0.53, C:0.19, G:0.05, T:0.23
Consensus pattern (32 bp):
AACATAGCATACATACATAAACAGTATTAAAC
Found at i:42443547 original size:20 final size:22
Alignment explanation
Indices: 42443503--42443548 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
42443493 ATCTTTTTGT
42443503 TTAAAAATTGATTCAATTCTATTA
1 TTAAAAATTGATTCAA-T-TATTA
42443527 TTAAAAATTGATTCATATTATT
1 TTAAAAATTGATTCA-ATTATT
42443549 GACATAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 16 0.76
25 1 0.05
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (22 bp):
TTAAAAATTGATTCAATTATTA
Found at i:42444509 original size:18 final size:18
Alignment explanation
Indices: 42444486--42444526 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
42444476 TTCTTTTTAT
*
42444486 AAAATTTAA-AAAATTAA
1 AAAATTTAACAAAAATAA
42444503 CAAAA-TTAACAAAAATAA
1 -AAAATTTAACAAAAATAA
42444521 AAAATT
1 AAAATT
42444527 ATAGAAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTTAACAAAAATAA
Found at i:42448749 original size:24 final size:24
Alignment explanation
Indices: 42448734--42448811 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 24
42448724 AGTTGCATAA
*
42448734 TCAGATTCAGACACAGATGCATGT
1 TCAGATTCAAACACAGATGCATGT
*
42448758 TCAGATTCAAACATAGATGCATGT
1 TCAGATTCAAACACAGATGCATGT
*
42448782 TCAGATTCAAATACA-ATTGCATGT
1 TCAGATTCAAACACAGA-TGCATGT
*
42448806 TTAGAT
1 TCAGAT
42448812 CCTACCCCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (24 bp):
TCAGATTCAAACACAGATGCATGT
Found at i:42453115 original size:12 final size:12
Alignment explanation
Indices: 42453095--42453129 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
42453085 ACCCACAAAC
42453095 TAATGAAAATAA
1 TAATGAAAATAA
*
42453107 TAATTAAAATAA
1 TAATGAAAATAA
42453119 TAATGGAAAAT
1 TAAT-GAAAAT
42453130 TATCAATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (12 bp):
TAATGAAAATAA
Found at i:42467809 original size:25 final size:25
Alignment explanation
Indices: 42467761--42467833 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
42467751 CTCTTCGCAG
* *
42467761 CTTCCCAATATTGGCTTATTTGAAT
1 CTTCCCAATATTGGCTCATATGAAT
* *
42467786 CTTCCCGATATTGGCTCGTATGAA-
1 CTTCCCAATATTGGCTCATATGAAT
* * *
42467810 CTTACCATTACATGGCTCATATGA
1 CTTCCCAATA-TTGGCTCATATGA
42467834 GCTTCCTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 7 0.18
25 31 0.82
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (25 bp):
CTTCCCAATATTGGCTCATATGAAT
Found at i:42467844 original size:25 final size:25
Alignment explanation
Indices: 42467797--42467852 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
42467787 TTCCCGATAT
*
42467797 TGGCTCGTATGAACTTACCATTACA
1 TGGCTCATATGAACTTACCATTACA
* *
42467822 TGGCTCATATGAGCTT-CCTATTATA
1 TGGCTCATATGAACTTACC-ATTACA
42467847 TGGCTC
1 TGGCTC
42467853 GAAAGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (25 bp):
TGGCTCATATGAACTTACCATTACA
Found at i:42474840 original size:17 final size:17
Alignment explanation
Indices: 42474814--42474850 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
42474804 ATGCACTGAT
*
42474814 ATGAATATGTAATGACA
1 ATGAAAATGTAATGACA
42474831 ATGAAAATGTAATGACA
1 ATGAAAATGTAATGACA
42474848 ATG
1 ATG
42474851 TACACTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (17 bp):
ATGAAAATGTAATGACA
Found at i:42480675 original size:229 final size:230
Alignment explanation
Indices: 42480266--42480724 Score: 740
Period size: 229 Copynumber: 2.0 Consensus size: 230
42480256 TGCCTCGTAT
* *
42480266 TCAAGTATGATAAAATCAGCTGAAAAAATGAATACATCCATACAAACTAAAATATCTTTCATTTA
1 TCAAGTATGATAAAATCAGCCGAAAAAATAAATACATCCATACAAACTAAAATATCTTTCATTTA
* *
42480331 CCCTTCAAGTTGAGCTAAAGATCAATCTGCAAGTTGCAATGTCACTGTAATGAGTTTCATATGAC
66 CCCTTCAAGTTGAGCTAAAAATCAATCTGCAAGTTGCAATGTCACTGTAATGAGTTTCATATAAC
* * *
42480396 CAATTCCCAACTTTCTAAAAGTAGATAGTGGCATGAGACTAATTCTAGCTCCC-AATTGCATAAA
131 CAATTCCCAACTTTCTAAAAGTAGATAATGGCATGAGACTAATGCTAGCTCCCAAATCGCATAAA
*
42480460 GCTTTTCCCAAATAATGATTTCCAATCGAACATAG
196 GCTTTGCCCAAATAATGATTTCCAATCGAACATAG
* ** * *
42480495 TCAAGTATGATAAAATCAGCCGGAAAAATAAATTTATCCATACGAACTAAAATATCTTTCATTTT
1 TCAAGTATGATAAAATCAGCCGAAAAAATAAATACATCCATACAAACTAAAATATCTTTCATTTA
* * *
42480560 CCCTTCAAGTTGAGCTAAAAATCGATCTGCAAGTTGTAATGTCACTGTAATGGGTTTCATATAAC
66 CCCTTCAAGTTGAGCTAAAAATCAATCTGCAAGTTGCAATGTCACTGTAATGAGTTTCATATAAC
* *
42480625 CAATTCCCAACTTTCTAAAAGTAGATAATGGCATGAGATTGATGCTAGCTCCCAAATCGCATAAA
131 CAATTCCCAACTTTCTAAAAGTAGATAATGGCATGAGACTAATGCTAGCTCCCAAATCGCATAAA
*
42480690 GCTTTGCCCAAATATTGATTTCCAATCGAACATAG
196 GCTTTGCCCAAATAATGATTTCCAATCGAACATAG
42480725 AATGGTAAAG
Statistics
Matches: 210, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
229 167 0.80
230 43 0.20
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (230 bp):
TCAAGTATGATAAAATCAGCCGAAAAAATAAATACATCCATACAAACTAAAATATCTTTCATTTA
CCCTTCAAGTTGAGCTAAAAATCAATCTGCAAGTTGCAATGTCACTGTAATGAGTTTCATATAAC
CAATTCCCAACTTTCTAAAAGTAGATAATGGCATGAGACTAATGCTAGCTCCCAAATCGCATAAA
GCTTTGCCCAAATAATGATTTCCAATCGAACATAG
Found at i:42489609 original size:92 final size:91
Alignment explanation
Indices: 42489484--42489806 Score: 271
Period size: 92 Copynumber: 3.5 Consensus size: 91
42489474 TACAATGGCA
* * * * * *
42489484 AATCTTATCTCTCTGAATTTGTAGTGGGGCAAGATAAAGTTACAACATTAAATATGGTTTTCTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAGCTACAACATTAAATAT-GTTTTCTTG
42489549 AAGTTGCAGTGAAATGGATAAAGTAGC
65 AAGTTGCAGTGAAATGGATAAAGTAGC
* * * * * *** * *
42489576 AATATTATCTCCTTAAAGTTGTAGTGGAGCAAGATGAAGCTACAA-A--ACATA--TACCCCTAA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAGCTACAACATTAAATATGTTTTCTTGA
* * ***
42489636 AGCTGTAGTGGGTTGGAATAAAGCTACAATGGC
66 AGTTGCAGTGAAATGG-ATAAAG-T---A--GC
*
42489669 AAATCTTATCTCCCTAAAGTTGCAGT-GAGGCAAGATAAAGCTACAACATTAAATCTAGTTTTCT
1 -AATCTTATCTCCCTAAAGTTGCAGTGGA-GCAAGATAAAGCTACAACATTAAATAT-GTTTTCT
* *
42489733 TGAAGTTGCAGTGAAATAGATAAAGCAGC
63 TGAAGTTGCAGTGAAATGGATAAAGTAGC
* *
42489762 AATCTTATCTCCCTAAAGTTGCAATGGAGCAAGATGAAGCTACAA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAGCTACAA
42489807 ATACTATACC
Statistics
Matches: 176, Mismatches: 39, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
86 15 0.09
87 6 0.03
88 1 0.01
89 4 0.02
91 2 0.01
92 77 0.44
93 8 0.05
94 38 0.22
95 2 0.01
97 3 0.02
99 6 0.03
100 14 0.08
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (91 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAGCTACAACATTAAATATGTTTTCTTGA
AGTTGCAGTGAAATGGATAAAGTAGC
Found at i:42489650 original size:186 final size:185
Alignment explanation
Indices: 42489417--42489900 Score: 662
Period size: 186 Copynumber: 2.6 Consensus size: 185
42489407 AATGCAGTAA
* * * * * *
42489417 AGCAAGATGAAGTTATAAATCCTATACCCTTAAATTTATAATGGGTTGGAATGCAGCTACAATGG
1 AGCAAGATGAAGCTACAAA-ACTATACCCTTAAAGTTGTAATGGGTTGGAATGAAGCTACAATGG
* * * * * *
42489482 CAAATCTTATCTCTCTGAATTTGTAGTGGGGCAAGATAAAGTTACAACATTAAATATGGTTTTCT
65 CAAATCTTATCTCCCTAAAGTTGCAGTGGGGCAAGATAAAGCTACAACATTAAATATAGTTTTCT
* * * * *
42489547 TGAAGTTGCAGTGAAATGGATAAAGTAGCAATATTATCTCCTTAAAGTTGTAGTGG
130 TGAAGTTGCAGTGAAATAGATAAAGCAGCAATATTATCTCCCTAAAGTTGCAATGG
* * * *
42489603 AGCAAGATGAAGCTACAAAACATATACCCCTAAAGCTGTAGTGGGTTGGAATAAAGCTACAATGG
1 AGCAAGATGAAGCTACAAAAC-TATACCCTTAAAGTTGTAATGGGTTGGAATGAAGCTACAATGG
* *
42489668 CAAATCTTATCTCCCTAAAGTTGCAGTGAGGCAAGATAAAGCTACAACATTAAATCTAGTTTTCT
65 CAAATCTTATCTCCCTAAAGTTGCAGTGGGGCAAGATAAAGCTACAACATTAAATATAGTTTTCT
*
42489733 TGAAGTTGCAGTGAAATAGATAAAGCAGCAATCTTATCTCCCTAAAGTTGCAATGG
130 TGAAGTTGCAGTGAAATAGATAAAGCAGCAATATTATCTCCCTAAAGTTGCAATGG
* * * *
42489789 AGCAAGATGAAGCTACAAATACTATACCCTTAAAGTTGCATTGGGTTGGAGTGAAGCTACAATAG
1 AGCAAGATGAAGCTACAAA-ACTATACCCTTAAAGTTGTAATGGGTTGGAATGAAGCTACAATGG
* * *
42489854 CGAATCTTGTCTCCCTAAAGTTGCAGTGGAGCAAGATAAAGCTACAA
65 CAAATCTTATCTCCCTAAAGTTGCAGTGGGGCAAGATAAAGCTACAA
42489901 ATCCCGTATC
Statistics
Matches: 261, Mismatches: 35, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
185 1 0.00
186 258 0.99
187 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (185 bp):
AGCAAGATGAAGCTACAAAACTATACCCTTAAAGTTGTAATGGGTTGGAATGAAGCTACAATGGC
AAATCTTATCTCCCTAAAGTTGCAGTGGGGCAAGATAAAGCTACAACATTAAATATAGTTTTCTT
GAAGTTGCAGTGAAATAGATAAAGCAGCAATATTATCTCCCTAAAGTTGCAATGG
Found at i:42489690 original size:94 final size:93
Alignment explanation
Indices: 42489080--42489901 Score: 345
Period size: 93 Copynumber: 8.8 Consensus size: 93
42489070 CTCTCTGAAA
* * * * * *
42489080 TTGTAGTGGGTTAGAATGAAGCTACAATGGCAAGTTTTATCTCTCTGAAGTTGCAGTGGAGCAAG
1 TTGTAGTGGGTTGGAATAAAGCTACAAT-GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAG
** * * * *
42489145 ACAAAGCTACAAATCTTATA-TCCTGAAG
65 ATGAAGCTACAAAACATATACCCCTAAAG
** * * * * * * *
42489173 TTGTAGTGGAATAGATTGAAA-CTACAGTAGCAAATCTCATCTCTCTAAAGATACAGTGGAGCAA
1 TTGTAGTGGGTTGGAAT-AAAGCTACAAT-GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAA
* * * *
42489237 GATTAAGCTACGACCTCAAATCCTAT-CTTCCTGAAG
64 GATGAAGCTAC-A----AAA-CATATAC-CCCTAAAG
* *** *
42489273 TTGCAGTGAAATGG-ATAAAG-T---A-GC-AATCTTATCTCCCTAAAGTTGCAGTGGAGTAAGA
1 TTGTAGTGGGTTGGAATAAAGCTACAATGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGA
* * *
42489331 TGAAGTTACAAATCTTATACCCCTGAAA-
66 TGAAGCTACAAAACATATACCCCT-AAAG
* * * * **
42489359 TTGTAGTCGGTTGGAATGAAGCTATAAT-AATGAATCTTATCTCCCTGAAA--TGCAGTAAAGCA
1 TTGTAGTGGGTTGGAATAAAGCTACAATGCA--AATCTTATCTCCCT-AAAGTTGCAGTGGAGCA
* * * * * *
42489421 AGATGAAGTTATAAATCCTATACCCTTAAAT
63 AGATGAAGCTACAAAACATATACCCCTAAAG
* * ** * * * * *
42489452 TTATAATGGGTTGGAATGCAGCTACAATGGCAAATCTTATCTCTCTGAATTTGTAGTGGGGCAAG
1 TTGTAGTGGGTTGGAATAAAGCTACAAT-GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAG
* * * *** * *
42489517 ATAAAGTTACAACATTAAATATGGTTTTCTTGAAG
65 ATGAAGCTACAA-A--ACATA---TACCCCTAAAG
* *** * * *
42489552 TTGCAGTGAAATGG-ATAAAG-T---A-GC-AATATTATCTCCTTAAAGTTGTAGTGGAGCAAGA
1 TTGTAGTGGGTTGGAATAAAGCTACAATGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGA
42489610 TGAAGCTACAAAACATATACCCCTAAAG
66 TGAAGCTACAAAACATATACCCCTAAAG
*
42489638 CTGTAGTGGGTTGGAATAAAGCTACAATGGCAAATCTTATCTCCCTAAAGTTGCAGT-GAGGCAA
1 TTGTAGTGGGTTGGAATAAAGCTACAAT-GCAAATCTTATCTCCCTAAAGTTGCAGTGGA-GCAA
* ***
42489702 GATAAAGCTAC--AACAT-TAAATCT--AG
64 GATGAAGCTACAAAACATATACCCCTAAAG
* ** * * * * *
42489727 TTTTCTTGAAGTTGCAGTGAAATAGATA-AA-GCAGCAATCTTATCTCCCTAAAGTTGCAATGGA
1 TTGTAGTG-GGTTGGAAT--AA-AGCTACAATGCA--AATCTTATCTCCCTAAAGTTGCAGTGGA
*
42489790 GCAAGATGAAGCTACAAATAC-TATACCCTTAAAG
60 GCAAGATGAAGCTACAAA-ACATATACCCCTAAAG
* * * * * *
42489824 TTGCATTGGGTTGGAGTGAAGCTACAATAGCGAATCTTGTCTCCCTAAAGTTGCAGTGGAGCAAG
1 TTGTAGTGGGTTGGAATAAAGCTACAAT-GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAG
*
42489889 ATAAAGCTACAAA
65 ATGAAGCTACAAA
42489902 TCCCGTATCC
Statistics
Matches: 545, Mismatches: 126, Indels: 115
0.69 0.16 0.15
Matches are distributed among these distances:
86 31 0.06
87 16 0.03
88 2 0.00
89 10 0.02
90 9 0.02
91 8 0.01
92 125 0.23
93 145 0.27
94 121 0.22
95 11 0.02
96 9 0.02
97 9 0.02
98 7 0.01
99 9 0.02
100 33 0.06
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (93 bp):
TTGTAGTGGGTTGGAATAAAGCTACAATGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGA
TGAAGCTACAAAACATATACCCCTAAAG
Found at i:42490093 original size:237 final size:237
Alignment explanation
Indices: 42489821--42490378 Score: 819
Period size: 237 Copynumber: 2.4 Consensus size: 237
42489811 TATACCCTTA
* * * * *
42489821 AAGTTGCATTGGGTTGGAGTGAAGCTACAATAGCGAATCTTGTCTCCCTAAAGTTGCAGTGGAGC
1 AAGTTGCAGTAGGTTGGAATGAAGCTACAATAGCGAATCTTATCTCCCTAAAGTTGTAGTGGAGC
* *
42489886 AAGATAAAGCTACAAATCCCGTATCCCTGAAGATATAGTAGATCAGATTGAAACTACAATAGCAA
66 AAGATAAAGCTACAAATCCCGTATCCCTGAAGATACAATAGATCAGATTGAAACTACAATAGCAA
* * *
42489951 ATCTCATCTCCACAAAGACGCAATAGTGCAAGATAAAGCTACAATATTAAATCTAGTTTTCTTGA
131 ATCTCATCTCCACAAAGACACAATAGGGCAAGATAAAGCTACAACATTAAATCTAGTTTTCTTGA
* *
42490016 AGTTGCAATGAAACAGATAAAGCAGCAATTCCAATCCCCCTG
196 AGCTGCAATGAAACAGATAAAGCAACAATTCCAATCCCCCTG
* *
42490058 AAGTTGCAGTAGGTTGGAATGAAGCTACAATAGCGAATCTTATCTCACTGAAGTTGTAGTGGAGC
1 AAGTTGCAGTAGGTTGGAATGAAGCTACAATAGCGAATCTTATCTCCCTAAAGTTGTAGTGGAGC
* * * * *
42490123 AAGATAAAGTTAAAAATCTCGTATCCTTGAAGATGCAATAGATCAGATTGAAACTACAATAGCAA
66 AAGATAAAGCTACAAATCCCGTATCCCTGAAGATACAATAGATCAGATTGAAACTACAATAGCAA
* * * * *
42490188 ATCTCATCTCTACGAAGATACAATGGGGCAAGATAAAGCTACAACATTAAATCTGGTTTTCTTGA
131 ATCTCATCTCCACAAAGACACAATAGGGCAAGATAAAGCTACAACATTAAATCTAGTTTTCTTGA
* * *
42490253 AGCTGCAGTGAAACAGATAAAGCAACAATTCTAGTCCCCCTG
196 AGCTGCAATGAAACAGATAAAGCAACAATTCCAATCCCCCTG
* * * *
42490295 AAGTAGCAGTAGGTTGAAATGAAGCTACAATAGCGAATCTTATCTCCTTAAAATTGTAGTGGAGC
1 AAGTTGCAGTAGGTTGGAATGAAGCTACAATAGCGAATCTTATCTCCCTAAAGTTGTAGTGGAGC
* *
42490360 AAGATGAAGCTGCAAATCC
66 AAGATAAAGCTACAAATCC
42490379 TATACTCTTG
Statistics
Matches: 283, Mismatches: 38, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
237 283 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (237 bp):
AAGTTGCAGTAGGTTGGAATGAAGCTACAATAGCGAATCTTATCTCCCTAAAGTTGTAGTGGAGC
AAGATAAAGCTACAAATCCCGTATCCCTGAAGATACAATAGATCAGATTGAAACTACAATAGCAA
ATCTCATCTCCACAAAGACACAATAGGGCAAGATAAAGCTACAACATTAAATCTAGTTTTCTTGA
AGCTGCAATGAAACAGATAAAGCAACAATTCCAATCCCCCTG
Found at i:42493329 original size:31 final size:30
Alignment explanation
Indices: 42493281--42493343 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
42493271 ACTTTATATT
*
42493281 AATTTATTAAATTAAATTAAAAATGTTACTA
1 AATTTATTAAATAAAATTAAAAATGTTA-TA
* *
42493312 AATTTATTATAA-AAAATTATAAATTTTATA
1 AATTTATTA-AATAAAATTAAAAATGTTATA
42493342 AA
1 AA
42493344 AAAAATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.14
31 22 0.79
32 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (30 bp):
AATTTATTAAATAAAATTAAAAATGTTATA
Found at i:42493354 original size:19 final size:19
Alignment explanation
Indices: 42493318--42493355 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42493308 ACTAAATTTA
*
42493318 TTATAAAAAATTATAAATT
1 TTATAAAAAATAATAAATT
42493337 TTATAAAAAA-AATCAAATT
1 TTATAAAAAATAAT-AAATT
42493356 AAGAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TTATAAAAAATAATAAATT
Found at i:42493837 original size:51 final size:51
Alignment explanation
Indices: 42493779--42493880 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
42493769 TAGTTGACAA
*
42493779 AGTACAATATTATTTAATTACATAAACAATATAATGGTTTTGTTTTTTTAT
1 AGTACAATATTATTTAATTACATAAACAATATAATGGTTTTGCTTTTTTAT
42493830 AGTACAATATTATTTAATTACATAAACAATATAATGGTTTTGCTTTTTTAT
1 AGTACAATATTATTTAATTACATAAACAATATAATGGTTTTGCTTTTTTAT
42493881 TTAGTGGATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (51 bp):
AGTACAATATTATTTAATTACATAAACAATATAATGGTTTTGCTTTTTTAT
Found at i:42498319 original size:22 final size:20
Alignment explanation
Indices: 42498287--42498336 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
42498277 CTAGCCAGAA
42498287 TATATTATGTTATAAAAATTAAT
1 TATA-TATGTTA-AAAAA-TAAT
* *
42498310 TATATATGTTAAATAATATT
1 TATATATGTTAAAAAATAAT
42498330 TATATAT
1 TATATAT
42498337 ATTTATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 4 0.16
22 7 0.28
23 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
TATATATGTTAAAAAATAAT
Found at i:42502483 original size:5 final size:5
Alignment explanation
Indices: 42502473--42502498 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42502463 ATTTTAATAA
42502473 AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT A
42502499 GAGATGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:42503981 original size:60 final size:60
Alignment explanation
Indices: 42503888--42504012 Score: 250
Period size: 60 Copynumber: 2.1 Consensus size: 60
42503878 AAAGACCCTA
42503888 TACTTAAGTGTTTGTTCTAGTGTAATACCTATATTTTCAAAATGTCCAATTTAATTTTTG
1 TACTTAAGTGTTTGTTCTAGTGTAATACCTATATTTTCAAAATGTCCAATTTAATTTTTG
42503948 TACTTAAGTGTTTGTTCTAGTGTAATACCTATATTTTCAAAATGTCCAATTTAATTTTTG
1 TACTTAAGTGTTTGTTCTAGTGTAATACCTATATTTTCAAAATGTCCAATTTAATTTTTG
42504008 TACTT
1 TACTT
42504013 TGCTTCTTCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (60 bp):
TACTTAAGTGTTTGTTCTAGTGTAATACCTATATTTTCAAAATGTCCAATTTAATTTTTG
Found at i:42507101 original size:16 final size:16
Alignment explanation
Indices: 42507076--42507117 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
42507066 TTAATCATAT
* *
42507076 TTAAACATATTTATTA
1 TTAAATATATTTATAA
42507092 TTAAATATA-TTATAA
1 TTAAATATATTTATAA
42507107 TTAAAATATAT
1 TT-AAATATAT
42507118 AATTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATATATTTATAA
Found at i:42507124 original size:14 final size:15
Alignment explanation
Indices: 42507076--42507126 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42507066 TTAATCATAT
* *
42507076 TTAAACATATTTATTA
1 TTAAATATA-TTATAA
42507092 TTAAATATATTATAA
1 TTAAATATATTATAA
42507107 TTAAA-ATA-TATAA
1 TTAAATATATTATAA
*
42507120 TTTAATA
1 TTAAATA
42507127 AAATTCTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 9 0.29
14 4 0.13
15 10 0.32
16 8 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATATATTATAA
Found at i:42507215 original size:120 final size:120
Alignment explanation
Indices: 42507074--42507320 Score: 440
Period size: 120 Copynumber: 2.0 Consensus size: 120
42507064 ATTTAATCAT
*
42507074 ATTTAAACATATTTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
42507139 ATCAATATTCTTATATGAATTTACTCAAATAATAATATGTGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATA
42507195 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
42507260 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATA
*
42507315 TTTTAA
1 ATTTAA
42507321 TTAAAATATA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
120 117 0.97
121 4 0.03
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATA
Found at i:42507235 original size:16 final size:16
Alignment explanation
Indices: 42507191--42507237 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
42507181 TACTATAAAA
*
42507191 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
42507207 TATTATT-AAATATAT
1 TATAATTAAAATATAT
42507222 TATAATTAAAATATAT
1 TATAATTAAAATATAT
42507238 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:42507309 original size:61 final size:61
Alignment explanation
Indices: 42507124--42507311 Score: 176
Period size: 61 Copynumber: 3.1 Consensus size: 61
42507114 ATATAATTTA
* *
42507124 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATAATAATATGTGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
* * * * * * *
42507185 ATAAAA-T-ATAATTTAACATAATTATTATTAAAT--ATATTA-T-AATTAA-AATATATAAT-T
1 ATAAAATTCTTAA--TAA-TTAA-TATTCTTATATGAAT-TTACTCAAATAATAATATATGATAC
42507242 T
61 T
*
42507243 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
42507305 ATAAAAT
1 ATAAAAT
42507312 ATATTTTAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
57 9 0.09
58 7 0.07
59 23 0.24
60 11 0.11
61 31 0.32
62 6 0.06
63 9 0.09
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
Found at i:42507327 original size:16 final size:16
Alignment explanation
Indices: 42507305--42507344 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
42507295 ATATGATACT
42507305 ATAAAATATAT-TTTA
1 ATAAAATATATATTTA
42507320 ATTAAAATATATGATTTA
1 A-TAAAATATAT-ATTTA
42507338 ATAAAAT
1 ATAAAAT
42507345 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.05
16 10 0.45
17 6 0.27
18 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAAAATATATATTTA
Found at i:42507344 original size:17 final size:17
Alignment explanation
Indices: 42507292--42507344 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
42507282 CTCAAATCAT
*
42507292 AATATATGATACT-ATAA
1 AATATATGAT-TTAATAA
42507309 AATATAT--TTTAATTAA
1 AATATATGATTTAA-TAA
42507325 AATATATGATTTAATAA
1 AATATATGATTTAATAA
42507342 AAT
1 AAT
42507345 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 1 0.03
15 2 0.06
16 10 0.32
17 13 0.42
18 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
AATATATGATTTAATAA
Found at i:42507375 original size:120 final size:119
Alignment explanation
Indices: 42507086--42507367 Score: 365
Period size: 120 Copynumber: 2.4 Consensus size: 119
42507076 TTAAACATAT
* * *
42507086 TTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTT
1 TTATGATTAAATAAATTATAA-TAAAATATATAATCTAATAAAATTCTTAATAATCAATATTCTT
* *
42507151 ATATGAATTTACTCAAATAATAATATGTGATACTATAAAATATAATTTAACATAA
65 ATATGAATTTACTCAAATAATAATATATGATACTATAAAATATAATTTAACAAAA
* * * *
42507206 TTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTT
1 TTATGATTAAATAAATTATAA-TAAAATATATAATCTAATAAAATTCTTAATAATCAATATTCTT
* * *
42507271 ATATGAATTTACTCAAATCATAATATATGATACTATAAAATATATTTTAATTAAAA
65 ATATGAATTTACTCAAATAATAATATATGATACTATAAAATATAATTTAA-CAAAA
*
42507327 TATATGATTTAATAAAATT-TAA-AATAAT-TATAA-CTAATAAA
1 T-TATGATTAAAT-AAATTATAATAA-AATATATAATCTAATAAA
42507368 TTTTCTTATA
Statistics
Matches: 148, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
119 7 0.05
120 118 0.80
121 7 0.05
122 12 0.08
123 4 0.03
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (119 bp):
TTATGATTAAATAAATTATAATAAAATATATAATCTAATAAAATTCTTAATAATCAATATTCTTA
TATGAATTTACTCAAATAATAATATATGATACTATAAAATATAATTTAACAAAA
Found at i:42507393 original size:47 final size:46
Alignment explanation
Indices: 42507327--42507585 Score: 175
Period size: 47 Copynumber: 5.7 Consensus size: 46
42507317 TTAATTAAAA
* *
42507327 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTAT
* * * *
42507374 TATATGAATTTGTATAATTTAAAATAATAATTATTAAATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAAT-AATA-AATTTTAT
* * * *
42507422 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTTT
1 TATATGAATTTATATAATTT-AAAATAATT-ATAATAATAAATTTTAT
* * *
42507465 TATATGAATTTATATAATTTAAAATAATTAATATGTTATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATT-ATA-ATAATA-AATTTTAT
* * *
42507513 TA-ATG-A--TATATAATTTCATAA-AATTATTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATTA-TAATAATAAATTTTAT
42507556 TATATGAATTTATATAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
42507586 ATATTAAATA
Statistics
Matches: 161, Mismatches: 29, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
42 4 0.02
43 19 0.12
44 34 0.21
45 9 0.06
46 9 0.06
47 58 0.36
48 24 0.15
49 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTAT
Found at i:42507405 original size:13 final size:13
Alignment explanation
Indices: 42507387--42507429 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
42507377 ATGAATTTGT
42507387 ATAATTTAAAATA
1 ATAATTTAAAATA
*
42507400 ATAATTATTAAAT-
1 ATAATT-TAAAATA
42507413 ATAATTTAATAATA
1 ATAATTTAA-AATA
42507427 ATA
1 ATA
42507430 TATAATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 2 0.08
13 15 0.60
14 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATTTAAAATA
Found at i:42507409 original size:195 final size:185
Alignment explanation
Indices: 42507190--42507675 Score: 562
Period size: 182 Copynumber: 2.6 Consensus size: 185
42507180 ATACTATAAA
* * *
42507190 ATATAATTTAACATAATTATTATTAAATAT-ATTATAATTAA-AATATATAATTTAATAAAATTC
1 ATATAATTTAAAATAATAATTATTAAATATAATT-TAA-TAATAATATATAATTTCATAAAATTC
*
42507253 TTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATATT-
64 TTAATAATAAATATTCTTATATGAATTTACT-AAATCATAATATAT-A-A-T-T--AATATATTA
42507317 T-TAATTAAAATATATGATTTAATAAAATTT-AAAATAATTA-TAACTAATAAATTTTCTTATAT
122 TATAATT-AAATA-ATGA--T-ATAAAATTTCAAAA-AATTATTAA-TAATAAATTTTCTTATAT
42507379 GAATTT
180 GAATTT
*
42507385 GTATAATTTAAAATAATAATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
1 ATATAATTTAAAATAATAATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
* * * * * *
42507450 GATAATAAATTTTTTTATATGAATTTA-TATAAT-TTAA-A-ATAATTAATATGTTATATAATTT
66 AATAATAAATATTCTTATATGAATTTACTA-AATCATAATATATAATTAATATATTATATAATTA
* * *
42507511 AATAATGATATATAATTTCATAAAATTATTGATAATAAATTTTCTTATATGAATTT
130 AATAATGATATAAAATTTCAAAAAATTATTAATAATAAATTTTCTTATATGAATTT
* *
42507567 ATATAATTTAAAATAATTAA-TATTAAATATAATTTAATAATGATATATAATTTCATTAAATTCT
1 ATATAATTTAAAATAA-TAATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCT
*
42507631 TAATAATAAAATGTTCTTATATGAATTTACTAAAATCATAATATA
65 TAATAAT-AAATATTCTTATATGAATTTACT-AAATCATAATATA
42507676 ACTTGAGAAT
Statistics
Matches: 256, Mismatches: 21, Indels: 36
0.82 0.07 0.12
Matches are distributed among these distances:
182 100 0.39
183 28 0.11
184 4 0.02
185 15 0.06
186 6 0.02
187 7 0.03
188 1 0.00
189 1 0.00
190 1 0.00
191 2 0.01
192 1 0.00
193 4 0.02
194 7 0.03
195 76 0.30
196 3 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (185 bp):
ATATAATTTAAAATAATAATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
AATAATAAATATTCTTATATGAATTTACTAAATCATAATATATAATTAATATATTATATAATTAA
ATAATGATATAAAATTTCAAAAAATTATTAATAATAAATTTTCTTATATGAATTT
Found at i:42507458 original size:91 final size:91
Alignment explanation
Indices: 42507361--42507659 Score: 485
Period size: 91 Copynumber: 3.3 Consensus size: 91
42507351 TAATTATAAC
*
42507361 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAA-TAATTATTAAATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
42507425 TAATATATAATTTCATAAAATTCTTGA
65 TGATATATAATTTCATAAAATTCTTGA
* *
42507452 TAATAAATTTTTTTATATGAATTTATATAATTTAAAATAATTAATATGT-TATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATAT-TAAATATAATTTAATAA
*
42507516 TGATATATAATTTCATAAAATTATTGA
65 TGATATATAATTTCATAAAATTCTTGA
42507543 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
42507608 GATATATAATTTCATTAAATTCTTAA
66 GATATATAATTTCATAAAATTCTTGA
*
42507634 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
42507660 CTAAAATCAT
Statistics
Matches: 193, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
90 1 0.01
91 168 0.87
92 24 0.12
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:42507478 original size:10 final size:9
Alignment explanation
Indices: 42507463--42507528 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
42507453 AATAAATTTT
42507463 TTTATATGAA
1 TTTATAT-AA
42507473 TTTATATAA
1 TTTATATAA
*
42507482 TTTAAAATAA
1 TTT-ATATAA
42507492 -TTA-AT-A
1 TTTATATAA
42507498 TGTTATATAA
1 T-TTATATAA
42507508 TTTA-ATAA
1 TTTATATAA
*
42507516 TGATATATAA
1 T-TTATATAA
42507526 TTT
1 TTT
42507529 CATAAAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 9 0.20
9 15 0.33
10 19 0.41
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (9 bp):
TTTATATAA
Found at i:42507524 original size:18 final size:18
Alignment explanation
Indices: 42507488--42507533 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
42507478 ATAATTTAAA
*
42507488 ATAA-TTAAT-ATGTTAT
1 ATAATTTAATAATGATAT
42507504 ATAATTTAATAATGATAT
1 ATAATTTAATAATGATAT
*
42507522 ATAATTTCATAA
1 ATAATTTAATAA
42507534 AATTATTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 17 0.65
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
ATAATTTAATAATGATAT
Found at i:42511916 original size:35 final size:35
Alignment explanation
Indices: 42511869--42511979 Score: 105
Period size: 35 Copynumber: 3.1 Consensus size: 35
42511859 CACCTAGCGT
* *
42511869 TAGTCAAATAAACCGACGATAGGTGTGCCCTGCAC
1 TAGTCGAATAAACCGACGATAGGTGTGCCCTACAC
* * * * ** * * *
42511904 TAGTTGGATAAACTGACAATATTTTGCGCCCAACGC
1 TAGTCGAATAAACCGACGATA-GGTGTGCCCTACAC
*
42511940 TAGTCGAATAAACCGATGATAGGTGTGCCCTACAC
1 TAGTCGAATAAACCGACGATAGGTGTGCCCTACAC
42511975 TAGTC
1 TAGTC
42511980 AGATAAATCG
Statistics
Matches: 54, Mismatches: 21, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
35 30 0.56
36 24 0.44
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (35 bp):
TAGTCGAATAAACCGACGATAGGTGTGCCCTACAC
Found at i:42511985 original size:71 final size:71
Alignment explanation
Indices: 42511864--42512099 Score: 219
Period size: 71 Copynumber: 3.3 Consensus size: 71
42511854 TTTTACACCT
* * * * *
42511864 AGCGTTAGTCAAATAAACCGACGATAGGTGTGCCCTGCACTAGTTGGATAAACTGACAATATTTT
1 AGCGCTAGTCGAATAAACCGATGATAGGTGTGCCCTACACTAGTCGGATAAACTGACAATATTTT
42511929 GCGCCC
66 GCGCCC
* * *
42511935 AACGCTAGTCGAATAAACCGATGATAGGTGTGCCCTACACTAGTCAGATAAA-TCGACAATGTTT
1 AGCGCTAGTCGAATAAACCGATGATAGGTGTGCCCTACACTAGTCGGATAAACT-GACAATATTT
*
42511999 TGCGGCC
65 TGCGCCC
* * * * *
42512006 AGCACTAGTC-AGATAAATCGAAAATGTCAAATGTGTG-CCTAGCACTAGTCGGATAAACCGACA
1 AGCGCTAGTCGA-ATAAACCG---ATG--ATAGGTGTGCCCTA-CACTAGTCGGATAAACTGACA
*
42512069 ATGA-ATTGCGCCC
59 AT-ATTTTGCGCCC
*
42512082 AGCGCTAGTCGGATAAAC
1 AGCGCTAGTCGAATAAAC
42512100 TGAAAATGTC
Statistics
Matches: 132, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
70 2 0.02
71 75 0.57
74 3 0.02
75 4 0.03
76 48 0.36
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (71 bp):
AGCGCTAGTCGAATAAACCGATGATAGGTGTGCCCTACACTAGTCGGATAAACTGACAATATTTT
GCGCCC
Found at i:42512061 original size:40 final size:39
Alignment explanation
Indices: 42512004--42512117 Score: 128
Period size: 36 Copynumber: 2.9 Consensus size: 39
42511994 TGTTTTGCGG
*
42512004 CCAGCACTAGTCAGATAAATCGAAAATGTCAAATGTGTGC
1 CCAGCACTAGTCGGATAAA-CGAAAATGTCAAATGTGTGC
* * *
42512044 CTAGCACTAGTCGGATAAACCGACAATG---AAT-TGCGC
1 CCAGCACTAGTCGGATAAA-CGAAAATGTCAAATGTGTGC
*
42512080 CCAGCGCTAGTCGGATAAACTGAAAATGTCAAATGTGT
1 CCAGCACTAGTCGGATAAAC-GAAAATGTCAAATGTGT
42512118 TTACGTAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
35 1 0.02
36 27 0.45
37 3 0.05
39 3 0.05
40 26 0.43
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (39 bp):
CCAGCACTAGTCGGATAAACGAAAATGTCAAATGTGTGC
Found at i:42512068 original size:76 final size:76
Alignment explanation
Indices: 42511962--42512117 Score: 217
Period size: 76 Copynumber: 2.1 Consensus size: 76
42511952 CCGATGATAG
* ** *
42511962 GTGTGCCCTACACTAGTCAGATAAATCGACAATGTTTTGCGGCCAGCACTAGTCAGATAAA-TCG
1 GTGTGCCCTACACTAGTCAGATAAACCGACAATGAATTGCGCCCAGCACTAGTCAGATAAACT-G
42512026 AAAATGTCAAAT
65 AAAATGTCAAAT
* * *
42512038 GTGTG-CCTAGCACTAGTCGGATAAACCGACAATGAATTGCGCCCAGCGCTAGTCGGATAAACTG
1 GTGTGCCCTA-CACTAGTCAGATAAACCGACAATGAATTGCGCCCAGCACTAGTCAGATAAACTG
42512102 AAAATGTCAAAT
65 AAAATGTCAAAT
42512114 GTGT
1 GTGT
42512118 TTACGTAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
75 4 0.06
76 66 0.93
77 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (76 bp):
GTGTGCCCTACACTAGTCAGATAAACCGACAATGAATTGCGCCCAGCACTAGTCAGATAAACTGA
AAATGTCAAAT
Found at i:42512099 original size:36 final size:36
Alignment explanation
Indices: 42511895--42512099 Score: 128
Period size: 36 Copynumber: 5.6 Consensus size: 36
42511885 CGATAGGTGT
* * * *
42511895 GCCCTGCACTAGTTGGATAAACTGACAAT-ATTTTGC
1 GCCCAGCACTAGTCGGATAAACCGACAATGA-ATTGC
* * * ** ** *
42511931 GCCCAACGCTAGTCGAATAAACCGATGAT-AGGTGT
1 GCCCAGCACTAGTCGGATAAACCGACAATGAATTGC
* * **
42511966 GCCCTA-CACTAGTCAGATAAATCGACAATGTTTTGC
1 GCCC-AGCACTAGTCGGATAAACCGACAATGAATTGC
* * * * *
42512002 GGCCAGCACTAGTCAGATAAATCGAAAATGTCAAATGTGT
1 GCCCAGCACTAGTCGGATAAACCGACAATG---AAT-TGC
*
42512042 GCCTAGCACTAGTCGGATAAACCGACAATGAATTGC
1 GCCCAGCACTAGTCGGATAAACCGACAATGAATTGC
*
42512078 GCCCAGCGCTAGTCGGATAAAC
1 GCCCAGCACTAGTCGGATAAAC
42512100 TGAAAATGTC
Statistics
Matches: 128, Mismatches: 34, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
35 24 0.19
36 73 0.57
37 3 0.02
39 1 0.01
40 27 0.21
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (36 bp):
GCCCAGCACTAGTCGGATAAACCGACAATGAATTGC
Found at i:42516009 original size:158 final size:158
Alignment explanation
Indices: 42515716--42516036 Score: 608
Period size: 158 Copynumber: 2.0 Consensus size: 158
42515706 ATGTTTAACT
42515716 CAACAATTCATCTTATAATTATCATTTCACACATTTACCCCCCAACAATTTAATTTCATTCAATT
1 CAACAATTCATCTTATAATTATCATTTCACACATTTACCCCCCAACAATTTAATTTCATTCAATT
42515781 TAGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTA
66 TAGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTA
42515846 CAGAGTCCTAAAACAGTCCCTATACTACC
131 CAGAGTCCTAAAACAGTCCCTATACTA-C
*
42515875 CAACAATTCATCTTATAATTATCATTTCACACATTTA-CCCCCAACAATTTAATTTCATTTAATT
1 CAACAATTCATCTTATAATTATCATTTCACACATTTACCCCCCAACAATTTAATTTCATTCAATT
42515939 TAGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTA
66 TAGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTA
*
42516004 TAGAGTCCTAAAACAGTCCCTATACTAC
131 CAGAGTCCTAAAACAGTCCCTATACTAC
42516032 CAACA
1 CAACA
42516037 TTCTATAGTT
Statistics
Matches: 160, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
157 6 0.04
158 117 0.73
159 37 0.23
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (158 bp):
CAACAATTCATCTTATAATTATCATTTCACACATTTACCCCCCAACAATTTAATTTCATTCAATT
TAGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTA
CAGAGTCCTAAAACAGTCCCTATACTAC
Found at i:42516022 original size:78 final size:77
Alignment explanation
Indices: 42515782--42516022 Score: 167
Period size: 78 Copynumber: 3.1 Consensus size: 77
42515772 CATTCAATTT
42515782 AGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTAC
1 AGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTA-
42515847 AGAGTCCTAAAAC
65 AGAGTCCTAAAAC
* * ** * * **
42515860 AGTCCCTA--T-ACTACCCAA-CAATT--CATC-TTATAATTATCATTTCACACATT-TACCCCC
1 AGTCCATACTTCAATATTCAAGCAATTAACATCATTA-AATTA--A-AT--CTC-TTCT-CAACC
** * ***
42515917 AACAATTTAA-TTTCATTTAATTT
58 -A-AATTTAAGAGTC--CTAAAAC
42515940 AGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTAT
1 AGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTA-
42516005 AGAGTCCTAAAAC
65 AGAGTCCTAAAAC
42516018 AGTCC
1 AGTCC
42516023 CTATACTACC
Statistics
Matches: 113, Mismatches: 28, Indels: 44
0.61 0.15 0.24
Matches are distributed among these distances:
71 3 0.03
72 9 0.08
74 6 0.05
75 7 0.06
76 1 0.01
77 3 0.03
78 28 0.25
79 4 0.04
80 23 0.20
81 3 0.03
82 1 0.01
83 7 0.06
84 6 0.05
86 9 0.08
87 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (77 bp):
AGTCCATACTTCAATATTCAAGCAATTAACATCATTAAATTAAATCTCTTCTCAACCAAATTTAA
GAGTCCTAAAAC
Found at i:42517570 original size:66 final size:66
Alignment explanation
Indices: 42517445--42517570 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
42517435 TGTTGTATGT
* * * *
42517445 TAAATAGCTTATTAATGACTGTTTCTTGTATGCAAAAGGTTTTTTTTAATTAAGTATAAATATCG
1 TAAATAGCTTATTAATGACAGTTTCTTGTATGCAAAAGGTTTTTTCTAATCAAATATAAATATCG
42517510 A
66 A
* **
42517511 TAAATAGCTTATTAATGACAGTTTGTTGTATGTTAAA-GTTTTTTCT-ATACAAATAATAAA
1 TAAATAGCTTATTAATGACAGTTTCTTGTATGCAAAAGGTTTTTTCTAAT-CAAAT-ATAAA
42517571 GTTAAATACG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
64 2 0.04
65 11 0.22
66 38 0.75
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.44
Consensus pattern (66 bp):
TAAATAGCTTATTAATGACAGTTTCTTGTATGCAAAAGGTTTTTTCTAATCAAATATAAATATCG
A
Found at i:42518793 original size:90 final size:90
Alignment explanation
Indices: 42518693--42518953 Score: 310
Period size: 90 Copynumber: 2.9 Consensus size: 90
42518683 AATTATCTTA
* * *
42518693 CAGCTATTATCTGA-AATTATGTTGTGTACTCACAACCATCCGACACCGTATTCACCTGCAATTT
1 CAGCTATTATCT-ACAATTATGTTGTGTACTCACAACCATCCGACAACGTATTAACTTGCAATTT
42518757 TGGTGGTTCATCCACATATTATCCGG
65 TGGTGGTTCATCCACATATTATCCGG
* * ** *
42518783 CAGCTATTATCTACAATTATATTGTGTACTCACAATCATCCGGTAGCGTATTAACTTGCAATTTT
1 CAGCTATTATCTACAATTATGTTGTGTACTCACAACCATCCGACAACGTATTAACTTGCAATTTT
* * * *
42518848 AGTGGTTCATTCACATATTATTCTG
66 GGTGGTTCATCCACATATTATCCGG
* * * * * *
42518873 AAGTTATTATCTACAATTATGTTGTGTATTCACAAGCAT-CTAGCAACGTATTAACTTGCAACAT
1 CAGCTATTATCTACAATTATGTTGTGTACTCACAACCATCCGA-CAACGTATTAACTTGCAA-TT
*
42518937 TTGGTGATTCATCCACA
64 TTGGTGGTTCATCCACA
42518954 ACTCGGTGTG
Statistics
Matches: 144, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
89 2 0.01
90 127 0.88
91 15 0.10
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (90 bp):
CAGCTATTATCTACAATTATGTTGTGTACTCACAACCATCCGACAACGTATTAACTTGCAATTTT
GGTGGTTCATCCACATATTATCCGG
Found at i:42520680 original size:30 final size:30
Alignment explanation
Indices: 42520646--42520708 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
42520636 ACTTAACAAG
42520646 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
42520676 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
42520706 CAA
1 CAA
42520709 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:42521379 original size:22 final size:21
Alignment explanation
Indices: 42521347--42521407 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
42521337 CCAACCCGAA
42521347 TATATTATGTTATAA-AAATTAAT
1 TATA-TATGTTATAATAAA--AAT
42521370 TATATATGTTA-AATAAAAAT
1 TATATATGTTATAATAAAAAT
* *
42521390 TATATATATTATATTAAA
1 TATATATGTTATAATAAA
42521408 TCACTCACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.38
21 7 0.21
22 10 0.29
23 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TATATATGTTATAATAAAAAT
Found at i:42521406 original size:25 final size:24
Alignment explanation
Indices: 42521345--42521408 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
42521335 GTCCAACCCG
42521345 AATATATTATGTT--ATAAAAATT
1 AATATATTATGTTAAATAAAAATT
42521367 AAT-TATATATGTTAAATAAAAATT
1 AATATAT-TATGTTAAATAAAAATT
*
42521391 ATATATATTATATTAAAT
1 A-ATATATTATGTTAAAT
42521409 CACTCACCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 3 0.08
22 9 0.25
24 10 0.28
25 11 0.31
26 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
AATATATTATGTTAAATAAAAATT
Found at i:42523673 original size:196 final size:193
Alignment explanation
Indices: 42523256--42523673 Score: 414
Period size: 196 Copynumber: 2.2 Consensus size: 193
42523246 GAATTTAAAC
* * * * *
42523256 AAACGCCGCAATAGGT-AAGCAATAGCAGCGCTTTCCCTAAAACGTCGCAAAAGATCAAGCATTA
1 AAACGCCGCTATAGGTCAAGCAATAGCGGCACTTTCCATAAAACGCCGCAAAAGATCAAGCATTA
* * * *
42523320 GCGGCGCTTTTGAGAAAGCGCCGCAAAAAAGTTAAGCAAAACGACGTTTTTCTATTGAGCTTTAC
66 GCGGCGCTTTTGAGAAAACGCCACAAAAAAGTTAAGCAAAACGACCTTTTCCTATTGAGCTTTAC
* * * * *
42523385 GAACATTAATGGCACTTTTTAACAAACGCCGTAATATATCGAGCATTAGCGATGCTTATTGAG
131 GAACATTAACGGCACTTTTTAACAAACGCCGCAAAAGATCGAGCATTAGCGACGCTTATTGAG
* * * * * * * * *
42523448 AAATGGCACTAAAGATCAAGTAATAGCGGCACTTTCTATAAAACGCCGCTAAAGGTC-AGACATT
1 AAACGCCGCTATAGGTCAAGCAATAGCGGCACTTTCCATAAAACGCCGCAAAAGATCAAG-CATT
* * * * * *
42523512 AGCGGTGCTTTTTAGAAAACGCCATAAAAAAGTTGAGCAAAACGACCTCGTTTCCTTTTTGCGCT
65 AGCGGCGCTTTTGAGAAAACGCCACAAAAAAGTTAAGCAAAACGACCT--TTTCC-TATTGAGCT
* * * * *
42523577 TTACTGGA-ATTAACGGCGA-TTTTTAACAAATGCCGCAAAAGATTGAGCATTAGCGGCGCTTTT
127 TTAC-GAACATTAACGGC-ACTTTTTAACAAACGCCGCAAAAGATCGAGCATTAGCGACGCTTAT
42523640 TGTA-
190 TG-AG
* *
42523644 AAACGTCGCTATAGGTCAAGCATTAGCGGC
1 AAACGCCGCTATAGGTCAAGCAATAGCGGC
42523674 GCCGCAAAAA
Statistics
Matches: 177, Mismatches: 41, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
192 12 0.07
193 77 0.44
195 4 0.02
196 80 0.45
197 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (193 bp):
AAACGCCGCTATAGGTCAAGCAATAGCGGCACTTTCCATAAAACGCCGCAAAAGATCAAGCATTA
GCGGCGCTTTTGAGAAAACGCCACAAAAAAGTTAAGCAAAACGACCTTTTCCTATTGAGCTTTAC
GAACATTAACGGCACTTTTTAACAAACGCCGCAAAAGATCGAGCATTAGCGACGCTTATTGAG
Found at i:42523875 original size:14 final size:14
Alignment explanation
Indices: 42523844--42524298 Score: 82
Period size: 14 Copynumber: 31.0 Consensus size: 14
42523834 AAGCATTAGC
*
42523844 GGTTTAGGGATTT-G
1 GGTTTAGGG-TTTAA
*
42523858 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAA
** *
42523872 GGTTTATTGTTTAT
1 GGTTTAGGGTTTAA
* **
42523886 TGTTTATTGTTTAA
1 GGTTTAGGGTTTAA
* *
42523900 GGGTTGGGGTTTAA
1 GGTTTAGGGTTTAA
*** *
42523914 GGTTTATAATTTAT
1 GGTTTAGGGTTTAA
* * * *
42523928 GTTTTATGATTTAG
1 GGTTTAGGGTTTAA
* *
42523942 GGTTTA-GATGATAGA
1 GGTTTAGGGT-TTA-A
42523957 GG-TTAGTGGTTTAA
1 GGTTTAG-GGTTTAA
* *
42523971 GGATTATGCGGTTTAT
1 GGTTTA-G-GGTTTAA
* *
42523987 GGGTTATGGTTTAA
1 GGTTTAGGGTTTAA
* *
42524001 GGGTTGGGGTTTAA
1 GGTTTAGGGTTTAA
* *
42524015 GATTTGAGGG-ATATA
1 GGTTT-AGGGTTTA-A
*
42524030 -GATTAGGGGTTTAA
1 GGTTTA-GGGTTTAA
** * *
42524044 GCATTATGGTTTAT
1 GGTTTAGGGTTTAA
*
42524058 GGTTTATGGTTTAA
1 GGTTTAGGGTTTAA
* *
42524072 GGGTTGGGGTTTAA
1 GGTTTAGGGTTTAA
42524086 GGTTTA-GGTGTTAA
1 GGTTTAGGGT-TTAA
* *
42524100 GGGTTAGGGGTTAA
1 GGTTTAGGGTTTAA
*
42524114 GGGTTAGGGGTTTATA
1 GGTTTA-GGGTTTA-A
* * *
42524130 GTTTATAGCTCATGTTTTAT
1 GGTT-TAG-----GGTTTAA
* * **
42524150 GATTCAGTATTTAGA
1 GGTTTAGGGTTTA-A
*
42524165 GG-TTAGGGGTTAAA
1 GGTTTA-GGGTTTAA
*
42524179 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAA
* *
42524193 GGTTCAAGGG-TTAG
1 GGTT-TAGGGTTTAA
*
42524207 GGTTTAAGGTTTAA
1 GGTTTAGGGTTTAA
*
42524221 GTGTTAAGGGTTAATGGATA
1 G-GTTTAGGGTT--T--A-A
42524241 TGAGTTTAGGGTTTAA
1 -G-GTTTAGGGTTTAA
42524257 GGTTTAAGGG-TTAA
1 GGTTT-AGGGTTTAA
* *
42524271 GGTCTAGGGTTTAG
1 GGTTTAGGGTTTAA
*
42524285 GGTCTAGGGTTTAA
1 GGTTTAGGGTTTAA
42524299 AATTAATATG
Statistics
Matches: 325, Mismatches: 80, Indels: 72
0.68 0.17 0.15
Matches are distributed among these distances:
13 17 0.05
14 212 0.65
15 50 0.15
16 19 0.06
17 4 0.01
19 4 0.01
20 4 0.01
21 15 0.05
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.42
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:42523878 original size:7 final size:7
Alignment explanation
Indices: 42523858--42523947 Score: 54
Period size: 7 Copynumber: 12.9 Consensus size: 7
42523848 TAGGGATTTG
*
42523858 GGTTTAG
1 GGTTTAT
42523865 GGTTTAT
1 GGTTTAT
42523872 GGTTTAT
1 GGTTTAT
*
42523879 TGTTTAT
1 GGTTTAT
*
42523886 TGTTTAT
1 GGTTTAT
* *
42523893 TGTTTAA
1 GGTTTAT
* **
42523900 GGGTTGG
1 GGTTTAT
*
42523907 GGTTTAA
1 GGTTTAT
42523914 GGTTTAT
1 GGTTTAT
**
42523921 AATTTAT
1 GGTTTAT
*
42523928 GTTTTAT
1 GGTTTAT
* *
42523935 GATTTAG
1 GGTTTAT
42523942 GGTTTA
1 GGTTTA
42523948 GATGATAGAG
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 65 1.00
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (7 bp):
GGTTTAT
Found at i:42524082 original size:28 final size:29
Alignment explanation
Indices: 42524051--42524121 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
42524041 TAAGCATTAT
*
42524051 GGTTTATGGTTTATGGT-TTAAGGGTT-GG
1 GGTTTAAGGTTTA-GGTGTTAAGGGTTAGG
42524079 GGTTTAAGGTTTAGGTGTTAAGGGTTAGG
1 GGTTTAAGGTTTAGGTGTTAAGGGTTAGG
*
42524108 GG-TTAAGGGTTAGG
1 GGTTTAAGGTTTAGG
42524122 GGTTTATAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 3 0.08
28 32 0.82
29 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.42, T:0.39
Consensus pattern (29 bp):
GGTTTAAGGTTTAGGTGTTAAGGGTTAGG
Found at i:42524107 original size:71 final size:72
Alignment explanation
Indices: 42523951--42524111 Score: 211
Period size: 71 Copynumber: 2.2 Consensus size: 72
42523941 GGGTTTAGAT
* * *
42523951 GATAGAGGTTAGTGGTTTAAGGATTATGCGGTTTATGGGTTATGGTTTAAGGGTTGGGGTTTAAG
1 GATATAGGTTAGGGGTTTAAGCATTAT-CGGTTTATGGGTTATGGTTTAAGGGTTGGGGTTTAAG
42524016 ATTTGAGG
65 ATTTGAGG
* * *
42524024 GATATAGATTAGGGGTTTAAGCATTAT-GGTTTATGGTTTATGGTTTAAGGGTTGGGGTTTAAGG
1 GATATAGGTTAGGGGTTTAAGCATTATCGGTTTATGGGTTATGGTTTAAGGGTTGGGGTTTAAGA
42524088 TTT-AGG
66 TTTGAGG
*
42524094 TGTTA-AGGGTTAGGGGTT
1 -GATATA-GGTTAGGGGTT
42524112 AAGGGTTAGG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
70 4 0.05
71 51 0.65
73 23 0.29
ACGTcount: A:0.22, C:0.01, G:0.37, T:0.40
Consensus pattern (72 bp):
GATATAGGTTAGGGGTTTAAGCATTATCGGTTTATGGGTTATGGTTTAAGGGTTGGGGTTTAAGA
TTTGAGG
Found at i:42524126 original size:64 final size:62
Alignment explanation
Indices: 42524051--42524284 Score: 200
Period size: 64 Copynumber: 3.7 Consensus size: 62
42524041 TAAGCATTAT
* *
42524051 GGTTTATGGTTTATGGTTTAAGGGTTGGGGTTTAAGGTTTAGGTGTTAAGGGTTAGGGGTTAA
1 GGTTTAGGGTTTATGGTTTAAGGGTTAGGGTTTAAGGTTTA-GTGTTAAGGGTTAGGGGTTAA
* * * * * * * * * * *
42524114 GGGTTAGGGGTTTATAGTTTATA-GCTCATGTTTTATGATTCAGTATTTAGAGGTTAGGGGTTAA
1 GGTTTA-GGGTTTATGGTTTA-AGGGTTAGGGTTTAAGGTTTAGTGTTAAG-GGTTAGGGGTT-A
42524178 A
62 A
* ** * *
42524179 GGTTTAGGGTTTATGGTTCAAGGGTTAGGGTTTAAGGTTTAAGTGTTAAGGGTTAATGGATAT
1 GGTTTAGGGTTTATGGTTTAAGGGTTAGGGTTTAAGGTTT-AGTGTTAAGGGTTAGGGGTTAA
* * * *
42524242 GAGTTTAGGGTTTAAGGTTTAAGGGTTAAGGTCTAGGGTTTAG
1 G-GTTTAGGGTTTATGGTTTAAGGGTTAGGGTTTAAGGTTTAG
42524285 GGTCTAGGGT
Statistics
Matches: 130, Mismatches: 34, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
63 16 0.12
64 99 0.76
65 15 0.12
ACGTcount: A:0.23, C:0.02, G:0.35, T:0.40
Consensus pattern (62 bp):
GGTTTAGGGTTTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGTGTTAAGGGTTAGGGGTTAA
Found at i:42524126 original size:71 final size:71
Alignment explanation
Indices: 42523951--42524135 Score: 205
Period size: 71 Copynumber: 2.6 Consensus size: 71
42523941 GGGTTTAGAT
* * *
42523951 GATAGAGGTTAGTGGTTTAAGGATTATGCGGTTTATGGGTTATGGTTTAAGGGTTGGGGTTTAAG
1 GATATAGGTTAG-GGGTTAAGGATTA-GCGGTTTATGGTTTATGGTTTAAGGGTTGGGGTTTAAG
42524016 ATTTGAGG
64 ATTTGAGG
* * * *
42524024 GATATAGATTAGGGGTTTAAGCATTA-TGGTTTATGGTTTATGGTTTAAGGGTTGGGGTTTAAGG
1 GATATAGGTTAGGGG-TTAAGGATTAGCGGTTTATGGTTTATGGTTTAAGGGTTGGGGTTTAAGA
42524088 TTT-AGG
65 TTTGAGG
* * * *
42524094 TGTTA-AGGGTTAGGGGTTAAGGGTTAGGGGTTTATAGTTTAT
1 -GATATA-GGTTAGGGGTTAAGGATTAGCGGTTTATGGTTTAT
42524136 AGCTCATGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
70 12 0.13
71 62 0.65
72 2 0.02
73 19 0.20
ACGTcount: A:0.22, C:0.01, G:0.37, T:0.40
Consensus pattern (71 bp):
GATATAGGTTAGGGGTTAAGGATTAGCGGTTTATGGTTTATGGTTTAAGGGTTGGGGTTTAAGAT
TTGAGG
Found at i:42524189 original size:7 final size:7
Alignment explanation
Indices: 42524179--42524297 Score: 64
Period size: 7 Copynumber: 16.9 Consensus size: 7
42524169 AGGGGTTAAA
42524179 GGTTTAG
1 GGTTTAG
*
42524186 GGTTTAT
1 GGTTTAG
*
42524193 GGTTCAAG
1 GGTT-TAG
42524201 GG-TTAG
1 GGTTTAG
*
42524207 GGTTTAA
1 GGTTTAG
42524214 GGTTTAAG
1 GGTTT-AG
* *
42524222 TGTTAAG
1 GGTTTAG
* *
42524229 GGTTAAT
1 GGTTTAG
*
42524236 GG-ATATG
1 GGTTTA-G
*
42524243 AGTTTAG
1 GGTTTAG
*
42524250 GGTTTAA
1 GGTTTAG
42524257 GGTTTAAG
1 GGTTT-AG
*
42524265 GG-TTAA
1 GGTTTAG
*
42524271 GGTCTAG
1 GGTTTAG
42524278 GGTTTAG
1 GGTTTAG
*
42524285 GGTCTAG
1 GGTTTAG
42524292 GGTTTA
1 GGTTTA
42524298 AAATTAATAT
Statistics
Matches: 81, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
6 8 0.10
7 61 0.75
8 12 0.15
ACGTcount: A:0.23, C:0.03, G:0.36, T:0.39
Consensus pattern (7 bp):
GGTTTAG
Found at i:42524196 original size:21 final size:21
Alignment explanation
Indices: 42524172--42524298 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 21
42524162 AGAGGTTAGG
* *
42524172 GGTTAAAGGTTTAGGGTTTAT
1 GGTTTAAGGTTTAGGGTTTAA
* *
42524193 GGTTCAAGGGTTAGGGTTTAA
1 GGTTTAAGGTTTAGGGTTTAA
*
42524214 GGTTTAAGTGTTAAGGG-TTAA
1 GGTTTAAG-GTTTAGGGTTTAA
* *
42524235 TGG-ATATGAGTTTAGGGTTTAA
1 -GGTTTAAG-GTTTAGGGTTTAA
* * * *
42524257 GGTTTAAGGGTTAAGGTCTAG
1 GGTTTAAGGTTTAGGGTTTAA
* *
42524278 GGTTTAGGGTCTAGGGTTTAA
1 GGTTTAAGGTTTAGGGTTTAA
42524299 AATTAATATG
Statistics
Matches: 80, Mismatches: 22, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
21 65 0.81
22 15 0.19
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.38
Consensus pattern (21 bp):
GGTTTAAGGTTTAGGGTTTAA
Found at i:42524733 original size:20 final size:20
Alignment explanation
Indices: 42524710--42524748 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
42524700 CACCCAGCCC
42524710 CTAATTCCCTTTCCAAATCA
1 CTAATTCCCTTTCCAAATCA
42524730 CTAATTCCCTTTCCAAATC
1 CTAATTCCCTTTCCAAATC
42524749 CCTTCCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (20 bp):
CTAATTCCCTTTCCAAATCA
Found at i:42527259 original size:18 final size:19
Alignment explanation
Indices: 42527247--42527282 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
42527237 CAATAATATT
42527247 AGTAATAAT-AATAATAAC
1 AGTAATAATAAATAATAAC
42527265 AGTAATAATAAATAATAA
1 AGTAATAATAAATAATAA
42527283 AAGATGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (19 bp):
AGTAATAATAAATAATAAC
Found at i:42529068 original size:103 final size:101
Alignment explanation
Indices: 42528935--42529132 Score: 351
Period size: 103 Copynumber: 1.9 Consensus size: 101
42528925 ATTAATATGT
*
42528935 AACCTATATTAGTATGATATATAACCTACATTTCAAATTCAATACTAATAAGTTTTTAAATTTTA
1 AACCTATATTAGTATGATATATAACCTACATTTCAAAGTCAATACTAATAAGTTTTTAAATTTTA
*
42529000 AAAGTAATTATAATTATTATATTTTTAAATAACTTAA
66 AAAATAATTATAATTATTATA-TTTTAAATAACTTAA
*
42529037 AACCTATATTAGTATGGATATATAACCTACATTTCAAAGTCATTACTAATAAGTTTTTAAATTTT
1 AACCTATATTAGTAT-GATATATAACCTACATTTCAAAGTCAATACTAATAAGTTTTTAAATTTT
42529102 AAAAATAATTATAATTATTATATTTTAAATA
65 AAAAATAATTATAATTATTATATTTTAAATA
42529133 TTATATCACT
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 24 0.26
103 68 0.74
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.43
Consensus pattern (101 bp):
AACCTATATTAGTATGATATATAACCTACATTTCAAAGTCAATACTAATAAGTTTTTAAATTTTA
AAAATAATTATAATTATTATATTTTAAATAACTTAA
Found at i:42529211 original size:9 final size:9
Alignment explanation
Indices: 42529197--42529477 Score: 83
Period size: 9 Copynumber: 32.0 Consensus size: 9
42529187 CTAATTTCCC
*
42529197 CATAACATA
1 CATAACTTA
42529206 CATAACTTA
1 CATAACTTA
*
42529215 CATAATTTA
1 CATAACTTA
*
42529224 CATAA-ATA
1 CATAACTTA
* * *
42529232 TATATCATA
1 CATAACTTA
*
42529241 TCAAAACTTA
1 -CATAACTTA
42529251 CATAACTTA
1 CATAACTTA
*
42529260 CATAATTTA
1 CATAACTTA
42529269 CATAACTTTA
1 CATAAC-TTA
* *
42529279 AAGAA-TTGAAAA
1 CATAACTT----A
* *
42529291 AAAAACTTA
1 CATAACTTA
42529300 CATAACTTA
1 CATAACTTA
**
42529309 CATATTTTA
1 CATAACTTA
*
42529318 CATAA-ATA
1 CATAACTTA
* * *
42529326 TATATCATAAA
1 CATAAC-T-TA
*
42529337 TATAACTTA
1 CATAACTTA
*
42529346 CATAACATA
1 CATAACTTA
42529355 CATAA---A
1 CATAACTTA
* *
42529361 TATAATTTA
1 CATAACTTA
42529370 CATAA---A
1 CATAACTTA
*
42529376 TATAACTTA
1 CATAACTTA
42529385 CATAACTTA
1 CATAACTTA
42529394 CATAA--TA
1 CATAACTTA
*
42529401 CATAA-ATA
1 CATAACTTA
* * *
42529409 TATATCATA
1 CATAACTTA
42529418 TCATAACTTA
1 -CATAACTTA
42529428 CATAACTTA
1 CATAACTTA
**
42529437 TTTATACTTA
1 CATA-ACTTA
42529447 CATAA--TA
1 CATAACTTA
42529454 CATAA---A
1 CATAACTTA
*
42529460 TATAACTTA
1 CATAACTTA
42529469 CATAACTTA
1 CATAACTTA
42529478 TTTATACTTA
Statistics
Matches: 204, Mismatches: 44, Indels: 48
0.69 0.15 0.16
Matches are distributed among these distances:
6 15 0.07
7 14 0.07
8 17 0.08
9 120 0.59
10 25 0.12
11 6 0.03
12 5 0.02
13 2 0.01
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:42529309 original size:94 final size:84
Alignment explanation
Indices: 42529204--42529436 Score: 274
Period size: 94 Copynumber: 2.7 Consensus size: 84
42529194 CCCCATAACA
*
42529204 TACATAACTTACATAATTTACATAAATATATATCATATCAAAACTTACATAACTTACATAATTTA
1 TACATAACTTACATAATTTACATAAATATATATCATATCATAACTTACATAACTTACATAA---A
42529269 CATAACTTTAAAGAATTGAAAAAAAAACT
63 CATAA-TTT--A-AA-T--AAAAAAAACT
* * *
42529298 TACATAACTTACATATTTTACATAAATATATATCATAAAT-ATAACTTACATAACATACATAAAT
1 TACATAACTTACATAATTTACATAAATATATATCAT--ATCATAACTTACATAACTTACATAAAC
* * *
42529362 ATAATTTACATAAATATAACT
64 ATAATTTAAATAAAAAAAACT
42529383 TACATAACTTACATAA--TACATAAATATATATCATATCATAACTTACATAACTTA
1 TACATAACTTACATAATTTACATAAATATATATCATATCATAACTTACATAACTTA
42529437 TTTATACTTA
Statistics
Matches: 127, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
81 2 0.02
82 16 0.13
83 18 0.14
85 23 0.18
87 1 0.01
88 1 0.01
89 1 0.01
91 3 0.02
92 5 0.04
94 35 0.28
95 20 0.16
96 2 0.02
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (84 bp):
TACATAACTTACATAATTTACATAAATATATATCATATCATAACTTACATAACTTACATAAACAT
AATTTAAATAAAAAAAACT
Found at i:42529365 original size:15 final size:15
Alignment explanation
Indices: 42529347--42529389 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
42529337 TATAACTTAC
*
42529347 ATAACATACATAAAT
1 ATAACTTACATAAAT
*
42529362 ATAATTTACATAAAT
1 ATAACTTACATAAAT
42529377 ATAACTTACATAA
1 ATAACTTACATAA
42529390 CTTACATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAACTTACATAAAT
Found at i:42529406 original size:31 final size:34
Alignment explanation
Indices: 42529368--42529432 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
42529358 AAATATAATT
*
42529368 TACATAAATATA-A-CTTA-CATAACTTACATAA
1 TACATAAATATATATCATATCATAACTTACATAA
42529399 TACATAAATATATATCATATCATAACTTACATAA
1 TACATAAATATATATCATATCATAACTTACATAA
42529433 CTTATTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 12 0.40
32 1 0.03
33 3 0.10
34 14 0.47
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (34 bp):
TACATAAATATATATCATATCATAACTTACATAA
Found at i:42529447 original size:19 final size:19
Alignment explanation
Indices: 42529423--42529487 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
42529413 TCATATCATA
42529423 ACTTACATAACTTATTTAT
1 ACTTACATAACTTATTTAT
* **
42529442 ACTTACATAATACATAAATAT
1 ACTTACAT-A-ACTTATTTAT
42529463 AACTTACATAACTTATTTAT
1 -ACTTACATAACTTATTTAT
42529483 ACTTA
1 ACTTA
42529488 TAAATAAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 13 0.35
20 8 0.22
21 8 0.22
22 8 0.22
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (19 bp):
ACTTACATAACTTATTTAT
Found at i:42537516 original size:44 final size:40
Alignment explanation
Indices: 42537464--42537578 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 40
42537454 AATGAAGCGT
*
42537464 CGCTAAAGGTCATGTTATTTAACGGCGTTTGGTGATAAAAGCAC
1 CGCTAAAGGTCATGTTATTTAGCGGCGTTT--T-ATAAAA-CAC
* * *
42537508 CGCTAAAGGTCATGTTATCTAGCGGCGCTTTTTTTAAACAC
1 CGCTAAAGGTCATGTTATTTAGCGGCG-TTTTATAAAACAC
* *
42537549 TGCTAAAGGTCATGATATTTAGCGGCGTTT
1 CGCTAAAGGTCATGTTATTTAGCGGCGTTT
42537579 ATGTGGACAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
40 3 0.05
41 27 0.43
42 4 0.06
43 1 0.02
44 25 0.40
45 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (40 bp):
CGCTAAAGGTCATGTTATTTAGCGGCGTTTTATAAAACAC
Found at i:42537572 original size:41 final size:43
Alignment explanation
Indices: 42537438--42537578 Score: 137
Period size: 44 Copynumber: 3.3 Consensus size: 43
42537428 GAACGGTACT
* * **
42537438 TTTAGCGGCGTTTGAGA-ATGAAGCGTCGCTAAAGGTCATGTTA
1 TTTAGCGGCGTTTGTGATA-AAAGCACCGCTAAAGGTCATGTTA
*
42537481 TTTAACGGCGTTTGGTGATAAAAGCACCGCTAAAGGTCATGTTA
1 TTTAGCGGCGTTT-GTGATAAAAGCACCGCTAAAGGTCATGTTA
* * * * *
42537525 TCTAGCGGCGCTTT-T-TTTAAA-CACTGCTAAAGGTCATGATA
1 TTTAGCGGCG-TTTGTGATAAAAGCACCGCTAAAGGTCATGTTA
42537566 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
42537579 ATGTGGACAA
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
40 3 0.04
41 27 0.33
42 4 0.05
43 13 0.16
44 32 0.39
45 4 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGTTA
Found at i:42539398 original size:33 final size:33
Alignment explanation
Indices: 42539326--42539400 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
42539316 TCAAATCATG
*
42539326 TTTT-ATTTTTATGTAGTCAAATTTTTTTATTC
1 TTTTAATTTTTATGTAGTCAAATTCTTTTATTC
* *
42539358 TTCTAATTTTTATGTAGGT-AATATTCTTTTCTT-
1 TTTTAATTTTTATGTA-GTCAA-ATTCTTTTATTC
42539391 TTTTAATTTT
1 TTTTAATTTT
42539401 AATTTTCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 3 0.08
33 22 0.61
34 11 0.31
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (33 bp):
TTTTAATTTTTATGTAGTCAAATTCTTTTATTC
Found at i:42540253 original size:18 final size:17
Alignment explanation
Indices: 42540211--42540253 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
42540201 GCCTGATTCA
42540211 ATGTATTCTTCAATTTT
1 ATGTATTCTTCAATTTT
* *
42540228 ATAATATTCTTTCATTTTT
1 AT-GTATTC-TTCAATTTT
42540247 ATGTATT
1 ATGTATT
42540254 ATCATAGACG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 9 0.43
19 10 0.48
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.60
Consensus pattern (17 bp):
ATGTATTCTTCAATTTT
Found at i:42540636 original size:21 final size:22
Alignment explanation
Indices: 42540589--42540636 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
42540579 CTAAAATATA
**
42540589 GACCCTAAAACCCTAGACTTTG
1 GACCCTAAAACCCTAGACCATG
* *
42540611 TACCCT-AAACCTTAGACCATG
1 GACCCTAAAACCCTAGACCATG
42540632 GACCC
1 GACCC
42540637 ATGGTTCAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.21
Consensus pattern (22 bp):
GACCCTAAAACCCTAGACCATG
Found at i:42546832 original size:32 final size:30
Alignment explanation
Indices: 42546788--42546848 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
42546778 AAATTTTAAT
42546788 AAATAAAAAATATATAA-AATTATTAAATATTA
1 AAATAAAAAATATA-AATAA-TA-TAAATATTA
*
42546820 AAATAAATAATATAAATAATATAAATATT
1 AAATAAAAAATATAAATAATATAAATATT
42546849 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 8 0.30
31 4 0.15
32 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (30 bp):
AAATAAAAAATATAAATAATATAAATATTA
Found at i:42546836 original size:9 final size:9
Alignment explanation
Indices: 42546822--42546846 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42546812 AAATATTAAA
42546822 ATAAATAAT
1 ATAAATAAT
42546831 ATAAATAAT
1 ATAAATAAT
42546840 ATAAATA
1 ATAAATA
42546847 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAAATAAT
Found at i:42547341 original size:16 final size:17
Alignment explanation
Indices: 42547322--42547355 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
42547312 TATTTGTTTT
*
42547322 ATTTTAAATAA-ATAAA
1 ATTTTAAAAAAGATAAA
42547338 ATTTTAAAAAAGATAAA
1 ATTTTAAAAAAGATAAA
42547355 A
1 A
42547356 GACTCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATTTTAAAAAAGATAAA
Found at i:42547470 original size:76 final size:76
Alignment explanation
Indices: 42547390--42547537 Score: 278
Period size: 76 Copynumber: 1.9 Consensus size: 76
42547380 AAATGCTTTT
*
42547390 AAAAATATAAATATAAATTTCAAAATTCAATATTATCTAAATTGGATTGGTTAGCGGTTCACCAA
1 AAAAATATAAATATAAATTTCAAAATTCAATATTATCTAAATTGGATTGGTTAACGGTTCACCAA
42547455 TTTTTTTAATC
66 TTTTTTTAATC
*
42547466 AAAAATATAAATATAAATTTCAATATTCAATATTATCTAAATTGGATTGGTTAACGGTTCACCAA
1 AAAAATATAAATATAAATTTCAAAATTCAATATTATCTAAATTGGATTGGTTAACGGTTCACCAA
42547531 TTTTTTT
66 TTTTTTT
42547538 TATCTCTCAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (76 bp):
AAAAATATAAATATAAATTTCAAAATTCAATATTATCTAAATTGGATTGGTTAACGGTTCACCAA
TTTTTTTAATC
Found at i:42547641 original size:28 final size:26
Alignment explanation
Indices: 42547609--42547663 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
42547599 ATAACATTGA
*
42547609 ATTTTAAAATTTTTTATATTTTTAAAAC
1 ATTTTAAAA-TATTT-TATTTTTAAAAC
**
42547637 ATTTTTTAATATTTTATTTTTAAAAC
1 ATTTTAAAATATTTTATTTTTAAAAC
42547663 A
1 A
42547664 AATCATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.54
27 4 0.17
28 7 0.29
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTTAAAATATTTTATTTTTAAAAC
Found at i:42547652 original size:20 final size:18
Alignment explanation
Indices: 42547609--42547652 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
42547599 ATAACATTGA
42547609 ATTTT-AAAATTTTTTAT
1 ATTTTAAAAATTTTTTAT
42547626 ATTTTTAAAACATTTTTTAAT
1 A-TTTTAAAA-ATTTTTT-AT
42547647 ATTTTA
1 ATTTTA
42547653 TTTTTAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 4 0.17
19 3 0.13
20 12 0.52
21 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAAAAATTTTTTAT
Found at i:42547672 original size:26 final size:25
Alignment explanation
Indices: 42547620--42547677 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
42547610 TTTTAAAATT
** **
42547620 TTTTATATTTTTAAAACATTTTTTAA
1 TTTT-TATTTTTAAAACAAATCATAA
42547646 TATTTTATTTTTAAAACAAATCATAA
1 T-TTTTATTTTTAAAACAAATCATAA
42547672 TTTTTA
1 TTTTTA
42547678 AAATTTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.19
26 19 0.70
27 3 0.11
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTTATTTTTAAAACAAATCATAA
Found at i:42549075 original size:31 final size:32
Alignment explanation
Indices: 42549040--42549101 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
42549030 CTATGTTATA
**
42549040 ATATTA-ATAATTTTAATAATTAAGTA-AATAT
1 ATATTATATAATAATAA-AATTAAGTATAATAT
42549071 ATATTATATAATAATAAAATTAAGTATAATA
1 ATATTATATAATAATAAAATTAAGTATAATA
42549102 AAACAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (32 bp):
ATATTATATAATAATAAAATTAAGTATAATAT
Found at i:42551841 original size:41 final size:40
Alignment explanation
Indices: 42551796--42551922 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 40
42551786 TGTTAGAGTT
* *
42551796 TGAATTGAGTTAAACAGAAAAGAATCGATTTAAAACAATAA
1 TGAATTGA-TTAAACAGAAAAGAATTGATTCAAAACAATAA
*
42551837 TGAATTGATTCAAACA-ACAAAGAATTGAGTCAAAACAAT-A
1 TGAATTGATT-AAACAGA-AAAGAATTGATTCAAAACAATAA
* * * *
42551877 TACAATCGATTTAAAAAGTAAAGAATTGATTCAAAACAATAA
1 T-GAATTGA-TTAAACAGAAAAGAATTGATTCAAAACAATAA
42551919 TGAA
1 TGAA
42551923 ACTAAGATTG
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
40 5 0.07
41 62 0.87
42 4 0.06
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (40 bp):
TGAATTGATTAAACAGAAAAGAATTGATTCAAAACAATAA
Found at i:42551853 original size:20 final size:21
Alignment explanation
Indices: 42551817--42551922 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
42551807 AAACAGAAAA
* *
42551817 GAATCGATTTAAAACAATAAT
1 GAATTGATTCAAAACAATAAT
* *
42551838 GAATTGATTC-AAACAACAAA
1 GAATTGATTCAAAACAATAAT
*
42551858 GAATTGAGTCAAAACAAT-AT
1 GAATTGATTCAAAACAATAAT
* * * * *
42551878 ACAATCGATTTAAAA-AGTAAA
1 -GAATTGATTCAAAACAATAAT
42551899 GAATTGATTCAAAACAATAAT
1 GAATTGATTCAAAACAATAAT
42551920 GAA
1 GAA
42551923 ACTAAGATTG
Statistics
Matches: 63, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
20 31 0.49
21 32 0.51
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (21 bp):
GAATTGATTCAAAACAATAAT
Found at i:42551865 original size:61 final size:61
Alignment explanation
Indices: 42551797--42551911 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
42551787 GTTAGAGTTT
* * *
42551797 GAATTGAGT-TAAACAGA-AAAGAATCGATTTAAAACAATAATGAATTGATTCAAACAACAAA
1 GAATTGAGTCAAAACA-ATAAACAATCGATTTAAAA-AATAAAGAATTGATTCAAACAACAAA
* *
42551858 GAATTGAGTCAAAACAATATACAATCGATTTAAAAAGTAAAGAATTGATTCAAA
1 GAATTGAGTCAAAACAATAAACAATCGATTTAAAAAATAAAGAATTGATTCAAA
42551912 ACAATAATGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
61 27 0.57
62 20 0.43
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.24
Consensus pattern (61 bp):
GAATTGAGTCAAAACAATAAACAATCGATTTAAAAAATAAAGAATTGATTCAAACAACAAA
Done.